The Glycomics Ontology GlycO focuses on the glycoproteomics domain to model the structure and functions of glycans and glycoconjugates, the enzymes involved in their biosynthesis and modification, and the metabolic pathways in which they participate. GlycO is intended to provide both a schema and a sufficiently large knowledge base, which will allow classification of concepts commonly encountered in the field of glycobiology in order to facilitate automated reasoning and information analysis in this domain. A atom of the chemical element oxygen (atomic number 8). This canonical atom allows phosphates, which have several O atoms attached to a P atom, to be described. This canonical atom allows phosphates, which have several O atoms attached to a P atom, to be described. This canonical atom allows phosphates, which have several O atoms attached to a P atom, to be described. A linked_phosphate_residue contains only 3 oxygen atoms - the fourth O atom connected to the P atom belongs to the adjacent residue (e.g., a carbohydrate residue or another phosphate residue). An N-glycan_derived_oligoglycosyl_alditol that has antennae that originate with the addition of b-GlcpNAc residues to Man residues (e.g., by the action of GlcNAc transferases). A carbohydrate residue that is classified primarily by the positions of oxidized carbons in its structure. For example, a keto_sugar_residue has a carbonyl (oxidized) carbon (ketone) at a position other than C1. An aldo_residue has a carbonyl (aldehyde) at C1. An alditol residue has no oxidized carbons. Bisected N-glycans have a b-GlcpNAc residue that is attached to O4 of the core b-Manp residue (e.g., by GlcNAc-transferase III.) An atom in a specific chemical context within a nucleoside_base_residue A carbohydrate residue with an aldehyde at C1 The anomeric carbon of the reducing form of the sugar is a aldehyde aldo aldo CHEBI:24590 D-dRibf A 2-deoxy-D-ribofuranose residue alpha-D-galactose CHEBI:28061 a-D-Galp An alpha-D-galactopyranose residue a &945; D-Manp CHEBI:16024 A D-mannopyranose residue b-D-Xylp A beta-D-xylopyranose residue CHEBI:28161 &946; b A 6-deoxy-aldoHex_residue with galacto configuration Fuc galacto Fuc 1 1 A monoglycosyl moiety contains a single carbohydrate_residue. This moiety is glycosidically linked to another (presumably non-carboohydrate) moiety. An oxygen atom in a specific chemical context within a non-standard_residue A hydrolysis reaction that is catalyzed by an enzyme water A glycine residue Gly G A protein that catalyzes the transfer of a carbohydrate residue from a donor_substrate to an acceptor_substrate A beta-D-galactopyranose residue beta-D-galactose CHEBI:27667 b-D-Galp A D-galactose residue An organic carboxylic acid with an animo group on the alpha carbon. The building blocks of proteins are amino acids. In GlycO, instances of free amino acids are classified as amino_acid while amino acids that are part of a polypeptide are classified as amino_acid_residue. A molecule comprised predominantly of ribonucleotide_moieties, linked in a linear fashion by phosphodiester bonds. 5 A carbohydrate residue with 5 main-chain carbon atoms An isoleucine residue I Ile A atom of the chemical element phosphorous (atomic number 15). L-Araf An L-arabinofuranose residue N-acetyl-alpha-D-glucosamine a-D-GlcpNAc An N-acetyl-alpha-D-glucosamine residue with the anomeric configuration alpha A protein that is classified primarily by its biological or biochemical function. A carbohydrate residue with 6 main-chain carbon atoms, C1 as the anomeric carbon, and no oxygen atoms are missing 0 A molecule in whiich a significant protion is composed of lipid moieties (e.g. dolichol) Thr An L-trheonine residue T A molecule that is classified primarily by its capacity to act as the substrate of a glycosyl transferase that transfers a carbohydrate_residue or carbohydrate moiety from this molecule to another molecule. Although glycosyl transferases can catalyze bot the forward and backward reaction, the donor and acceptor are defined for the usual direction of the metabolic flux (i.e., biosynthesis of a glycan). 1 A carbohydrate residue that is classified primarily by the number of carbons in the main chain An L-aspartic acid residue Asp D A D-mannose residue a-D-GalpNAc An N-acetyl-alpha-D-galactosamine residue with the anomeric configuration alpha b-NeuAc A beta-N-acetyl-neuraminic acid residue An alpha-D-galactopyranosyl residue in the context of a monoglycosyl_moiety Having a five-membered ring, usually indicated by an italicized f. f o Not in a ring (as an alditol). THere is no shorthand nomenclature for this, but GLYDE uses "o" to specify an open chain form. Havig a six membered ring, indicated by an italicized p p A property that specifies the number of carbons in the ring that is part of a carbohydrate_residue's structure. A mannose residue Man manno A peptide containing only a few amino_acid_residues. 2 A free glycan is a carbohydrate that is not part of a glycocongugate. Examples are free oligosacharides and polysaccharides. 1 D A residue with the absolute configuration D An oligoglycosyl alditol derived from an N-glycan by enzymatic or chemical release from a glycoprotein/glycopeptide followed by reduction (e.g., with borohydride). The precursor of each of these oligoglycosyl alditols is an N-glycan_derived_oligosaccharide, whose precursor was an N-glycan. The residues of the N-glycan are the ultimate precursor residues for the residues in the oligoglycosyl alditol. An alpha-D-glucopyranosyl residue in the context of a monoglycosyl_moiety An L-arabinose residue L-Ara A carbohydrate residue with an aldehyde at C1 and six atoms in the ring (pyranose) a-L-Fucp An L-Fucp residue with the alpha anomeric configuration A nonreducing sugar residue with a 5-membered ring, usually represented by the italicized letter f. An N-glycan_derived_oligoglycosyl_alditol that has a b-D-GlcpNAc residue linked to O4 of the core b-D-Manp residue. A non-standard residue in a specific chemical context An N-glycan_derived_oligoglycosyl_alditol that has ONLY mannosyl residues attached to the core. A beta-D-ribofuranose residue An L-galactopyranose residue L-Galp A beta-L-fucopyranosyl residue in the context of a monoglycosyl_moiety 4 A carbohydrate residue with 4 main-chain carbon atoms A D-galactofuranose residue D-Galf A D-N-acetyl-galactosame residue with the pyranose ring form N-acetyl-D-galactosamine D-GalpNAc CHEBI:28037 A reducing N-acetyl-D-glucosame residue D-GlcNAc A peptide molecule that contains many amino_acid_residues. An L-proline residue P Pro An molecule consisting of a few carbohydrate_residues with a reducing-carbohydrate_residue at the reducing end A nitrogen atom in a specific chemical context within a non-standard_residue A beta-N-acetyl-alpha-D-galactosamine residue in the chemical context of an N-glycan N-acetyl-beta-D-galactosamine CHEBI:28497 b-D-GalpNAc gluco A carbohydrate residue that corresponds to a glucose in which O2 is replced by a nitrogen GlcN L-Galf An L-galactofuranose residue A glycosylated polypeptide (in which the peptide contains many amino_acid_residues). 1 An oligopeptide with an O-glycan attached to at least one serine, threonine, or hydroxyproline residue. A non-standard residue in the chemical context of an N-glycan A polysaccharide attached to a peptide. A carbohydrate residue with ketone at C2 and 6 carbons in the main chain CHEBI:28518 a-D-Xylp An alpha-D-xylopyranose residue A carbohydrate residue with ketone in the main chain An acidic amino acid residue 5-deoxy deoxy 3-deoxy deoxy An N-glycan_derived_oligosaccharide that has a b-D-GlcpNAc residue linked to O4 of the core b-D-Manp residue. A protein with a defined catalytic activity. 1 An oligopeptide with an N-glycan attached to N4 of at least one asparagine residue. A carbohydrate residue with 7 main-chain carbon atoms 7 A D-galactopyranose residue D-Galp D-galactose CHEBI:17118 A GlcN residue with the absolute configuration D D-GlcN An atom in a specific chemical context within a carbohydrate_residue A carbohydrate residue that is missing an oxygen, as it has been replaced by another atom, such as H or N L A residue with the absolute configuration L 1 A carbohydrate moiety is the carbohydrate portion of a molecule, defined by the restriction that it contains at least one sugar residue. To avoid recursion, sugar residues are not themselves defined as carbohydrate moieties, although the carbohydrate moiety can contain exactly one sugar residue. A ribose residue Rib ribo An oxygen atom in a specific chemical context within an amino_acid_residue CHEBI:17925 alpha-D-glucose An alpha-D-glucopyranose residue a-D-Glcp An alanine residue A Ala A 3-deoxy-D-manno-2-octulopyranosonic acid residue, commonly known as KDO D-KDOp D-dRib A 2-deoxy-D-ribose residue A beta-D-KDO residue b-D-KDOp A beta-D-2-deoxy-ribofuranosyl residue in the context of a nucleoside A molecular fragment that contains a ribose residue and a nucleoside_base residue. An alpha-N-glycolyl-neuraminic acid residue a-NeuGc A Fuc residue with absolute configuration L L-Fuc An atom or collection of atoms together form a chemical entity A molecular fragment that consists of a ribose residue, a nucleoside_base residue, and at least one linked_phosphate_residue. A (usually highly reactive) atomic or molecular entity that has unpaired electrons in a valence shell. b-L-Fucp An L-Fucp residue with the beta anomeric configuration N-acetyl N-acetyl 2-N-acetyl D-GalNAc A D-galactosame residue with an N-acetyl substituent GalNAc A beta-D-fructofuranose residue deoxy 2-deoxy A carbohydrate residue in which oxygen atom O2 is missing A hydrolysis reaction that is catalyzed by an enzyme and invloves the cleavage of a glycosidic bond. A carbohydrate residue in the chemical context of the glycan portion of an N-glycan. This includes all carbohydrate residues in N-glycans, their dol-P-P-linked precursors, and oligosaccharides released by cleavage of N-glycans The glycosidic oxygen - O1 - is part of the residue only when it is a reducing residue. For glycosyl residues, the glycosidic oxygen is formally specified as a component atom of the moiety to which the residue is covalently linked. For example, in the disaccharide maltose, O4 of the reducing glucose residue is also a glycosidic oxygen, and is not considered part of the (non-reducing) glucosyl residue that is linked to the reducing residue. A carbohydrate residue with an aldehyde at C1 that is not glycosidically linked to another moiety 0 An intramolecular_llink between two atoms A carbohydrate residue with 6 main-chain carbon atoms, C1 as the anomeric carbon, and oxygen atom O2 missing An alpha-L-galactofuranose residue a-L-Galf In hybrid N-glycans, the Mana1-6 arm contains only Man residues, while the Mana1-3 arm has antennae (each containing at least one b-GlcpNAc residue). . A glycoconjugate in which the non-carbohydrate moiety is primarily lipid A beta-D-xylopyranose residue in the chemical context of an N-glycan b-D-Xylp 0 0 0 0 0 0 0 The smallest piece of a chemical element, e.g., a carbon atom. 0 0 0 0 0 0 0 An molecule consisting of a few carbohydrate_residues with an alditol_residue at what would otherwise be the reducing end. A carbohydrate residue with an aldehyde at C1 and six main chain carbon atoms CHEBI:33917 A cysteine residue Cys C A carbon atom in a specific chemical context within an amino_acid_residue A glucosaminitol residue with the absolute configuration D D-glucosaminitol D-GlcN-ol An aromatic amino acid residue An alpha-D-mannopyranose residue in the chemical context of an N-glycan a-D-Manp An N-acetyl-alpha-D-glucosamine residue with the anomeric configuration beta b-D-GlcpNAc N-acetyl-beta-D-glucosamine CHEBI:28009 A chemical property of a residue that specifies its overall "handedness" . It s often designated as D or L for amino acids and sugars. Another class, the "sugar_configuration" specifies the configuration of all the assymetric centers for a carbohydrate_residue. A carbohydrate residue with ketone at C2, 6 carbons in the main chain, and no missing oxygen atoms D-Ribf A D-ribofuranose residue A galactose residue Gal CHEBI:18287 An a-L-Fucp residue in he context of an N-glycan a-L-Fucp b-D-dRibf A 2-deoxy-beta-D-ribofuranose residue An N-glycan_derived_oligoglycosyl_alditol in which the arm initiated with an alpha mannose attached to O6 of the core b-D-Manp residue contains only Man residues, while the the arm initiated with an alpha mannose attached to O3 of the core b-D-Manp residue has antennae (each containing at least one b-GlcpNAc residue). His H A histidine residue A sulfur-containing amino acid residue A biomolecule that has peptide moiety (amino acids connected by peptide bonds), plus a carbohydrate moiety. In GlycO, this class includes molecules with peptide moieties of different sizes, that is, it includes glycoproteins and glycopeptides. a-D-Manp An alpha-D-mannopyranose residue CHEBI:28729 An alpha-D-KDO residue a-D-KDOp S Ser A serine residue An alditol residue with 6 main chain carbons A molecular_property of an enzyme A molecule that is a biosynthetic precursor to N-linked glycans and contains a dolichol pyrophosphate aglycon. The N-glycan_core_a-D-GlcpNAc_A is linked to the pyrophosphate by an alpha-linkage. A biomolecule that is composed primarily of amino acids connected in a linear fashion by peptide bonds. In GlycO, oligopeptides (which contain only a few amino_acid_residues) and proteins (which contain many amino_acid_residues) are both classified as peptides. 1 a-D-Fruf An alpha-D-fructofuranose residue An alpha-D-N-acetyl-glucopyranosaminyl residue in the context of a monoglycosyl_moiety A molecue consisting of a single reducing_carbohydrate_residue. 1 A hydrogen atom in a specific chemical context within a nucleoside_base_residue H High-mannose N-glycans have ONLY mannosyl residues attached to the core. An alpha-N-glycolyl-neuraminic acid residue in the chemical context of an N-glycan a-NeuGc A carbohydrate residue with an aldehyde at C1 and five main chain carbon atoms An alpha-L-fucopyranosyl residue in the context of a monoglycosyl_moiety A beta-D-galactopyrano residue in the chemical context of an N-glycan CHEBI:27667 beta-D-galactose b-D-Galp A link between two molecular_fragments in the same molecule. The class intramolecular_link includes links between moieties (e.g., the link between a glycan_moiety and a peptidemoiety), between residues (e.g., between a mannose residue and a GlcNAc residue) and between atoms (e.g., between C1 of a mannose residue and O4 of a GlcNAc residue. Links are thus hierarchical, and a higher-order link embodies the lower-order links that specify more structural detail. A atom of the chemical element carbon (atomic number 6). a-NeuNAc An alpha-N-acetyl-neuraminic acid residue (pyranose) in the chemical context of an N-glycan a-Neup5Ac a-Neu5Ac CHEBI:17012 A atom of the chemical element hydrogen (atomic number 1). A molecular_property of a glycosyl transferase that specifies whether the reaction catalyzed by the enzyme results in the inversion of retention of the anomeric configuration of the carbohydrate_residue that is transferred. A molecule comprised predominantly of nucleotide_moieties (ribonucleotides and deoxyribonucleotides) 0 A chemical property of a carbohydrate_residue A lectin produced by a plant species A nonreducing sugar residue with a 6-membered ring, usually represented by the italicized letter p. A carbohydrate residue in the chemical context of the glycan portion of a glycolipid. This includes all carbohydrate residues in glycolipids and oligosaccharides released by cleavage of glycolipids. A carbohydrate residue with 5 main-chain carbon atoms, C1 as the anomeric carbon, and oxygen atom O2 missing A beta-D-ribofuranosyl residue in the context of a nucleoside A carbohydrate residue with 5 main-chain carbon atoms, C1 as the anomeric carbon, and no oxygen atoms are missing A D-glucopyranose residue D-Glcp CHEBI:17634 D-glucose A molecule comprised predominantly of deoxy-ribonucleotide_moieties, linked in a linear fashion by phosphodiester bonds. A basic amino acid residue D-Frucf A D-fructofuranose residue A molecular fragment that consists of a ribose residue, a nucleoside_base residue and 1 to 3 phosphate residues. In GlycO, a nucleotide is classified as a (phosphorylated) nucleoside. Thr T A threonine residue N-acetyl-D-glucosaminitol D-GlcNAc-ol A D-glucosaminitol residue with an N-acetyl substituent GlcNAc-ol A sugar_structural_variation that specifies the identity and location of atoms that replace an oxygen in the carbohydrate_residue. For example, a GlcN residue has two sugar_oxygen_replacement_variations: _2-amino and _2-deoxy. A D-ribose residue D-Rib D-GlcNAc GlcNAc A D-glucosame residue with an N-acetyl substituent An intramolecular link between one moiety and another moiety. A moiety_link embodies a residue_link, which itself embodies a covalent bond, which provides more detailed information regarding the link. For example, a moiety_link between a (monoglycosyl) a-D-Manp moiety and a UDP moiety embodies a residue_link between the a-D-Manp residue and the beta-phosphate residue, and this, in turn, embodies a glycosidic covalent bond betwen C1 of the a-D-Manp residue and O1 of the beta-phosphate residue. An N-glycan is an oligosaccharyl moiety that is linked to the delta nitrogen of an asparagine residue in a glycpeptide or glycoprotein. This class only includes the glycan part. When the N-glycan is released from its connection to the peptide, a free oligosaccharide is generated. The same N-glycan residues are used to define the free oligosaccharide (except a reducing residue must also be used), but the released oligosaccharide itself is no longer an N-glycan, it is of the class "oligosaccharide" a subclass of "free_glycan". A atom of the chemical element nitrogen (atomic number 7). Neu D-glycero-D-galacto A neuraminic acid residue A methionine residue M Met A carbohydrate residue with ketone at C2 and 5 atoms in the ring A carbohydrate residue with ketone at C2 and 8 carbons in the main chain 0 A carbohydrate residue with no aldehyde or ketone. alditolic alditolic R An arginine residue Arg A beta-L-galactopyranose residue b-L-Galp A molecular fragment that is the non-carbohydrate part of a glycoconjugate. A non-polar amino acid residue (e.g., valine, leucine) Manol Man-ol mannitol A mannitol residue An beta-N-glycolyl-neuraminic acid residue b-NeuGc A N-cyclic amino acid residue (e.g., prolne) A sugar_structural_variation that specifies the location of an oxygen that has been replaced in the carbohydrate_residue. If no other information is given (e.g., by specifying a sugar_amino_carbon_variation) then it is assumed that the oxygen atom has been replaced by a hydrogen atom. An alpha-D-mannopyranosyl residue in the context of a monoglycosyl_moiety CHEBI:28009 b-D-GlcpNAc A beta-N-acetyl-alpha-D-glucosamine residue in the chemical context of an N-glycan N-acetyl-b-D-glucosamine N-acetyl-beta-D-glucosamine A covalent_bond between the anomeric carbon of a carbohydrate residue and an oxygen or nitrogen atom of another residue or moiety. A phosphorous atom in a specific chemical context within a non-standard_residue An oxygen atom in a specific chemical context within a nucleoside_base_residue O A property that specifies structural variations of a carbohydrate_residue. For example, a sugar_structural_variation specifies whether the carbohydrate_residue is an aldose vs. a ketose, a deoxy-sugar, or if it bears a functional group such as an N-acetyl group. Glc A glucose residue Lys K A lysine residue An L-asparagine residue Asn N A carbohydrate residue that is not glycosidically linked to another moiety A carbohydrate residue that has a nitrogen atom attached to a main-chain carbon D-fru A D-fructose residue An atom in a specific chemical context within an amino_acid_residue A sulfur atom in a specific chemical context within a non-standard_residue A molecular fragment that contains more than one atom A lipid-linked_N-glycan_precursor_moiety is an oligosaccharyl moiety that is linked to the the pyrophosphate of dolichol pyrophosphate. This oligosaccharyl moiety is transferred to the nascent glycoprotein en bloc. This class only includes the glycan part. Each instance is a precursor of an N-glycan. The residues in this precursor are specified as precursor residues of the residues in the N-glycan. A non-standard_residue is a residue that is not a carbohydrate, amino acid or nucleotide. Examples are sulfates and phosphates. A non-standard residue is treated like any other residue, that is, it is an entity that is conceptually separated from the object to which it is attached, and it is linked to the other structure by an intramolecular_link. (See functional_group for a similar but contrasting concept.) A canoncical non-standard residue instance is like a canonical residue instance, in that it is defined by its chemical identity and its context within a canonical representation of a collection of related structures. For example, a canonical sulfate substituent may be linked to a specific position of a specific canonical N-glycan residue. A non-standard residue may be naturally occuring or synthetically introduced. For example, 2-aminopyridine may be a non-standard residue that is attached to the GlcNAc-ol residue of a derivatized N-glycan being analyzed by HPLC or CE. A molecule that has at least 1 glycan moiety and 1 non-carbohydrate_moiety. The carbohydrate moiety (by its own definition) has at least one carbohydrate_residue. 1 1 An alpha-L-galactopyranose residue a-L-Galp A carbohydrate residue with an aldehyde at C1 and a five-membered ring O An oxygen atom in a specific chemical context within a carbohydrate_residue A carbohydrate residue with ketone at C2 and 6 atoms in the ring A lectin produced by a microbial species An arabinose residue Ara arabino Ara A molecule in whiich a significant protion is composed of carbohydrate residues. Glycocongugates are included in the carbohydrate class, just as glycoproteins are incuded in the protein class 0 b-D-GalpNAc CHEBI:28497 An N-acetyl-alpha-D-galactosamine residue with the anomeric configuration beta N-acetyl-beta-D-galactosamine A carbon atom in a specific chemical context within a non-standard_residue A residue consisting of a single lipid, for example dolichol. A carbohydrate residue with ketone at C3 that is not glycosidically linked to another moiety An epitope is the chemical structure that is recognized by an antibody b-L-Galf A beta-L-galactofuranose residue uronic uronic A carbohydrate residue with an alehyde at C1 and a carboxylic acid at the highest numbered carbon in the main chain A transformation in which reactants are converted to products, usually by the recombination of atoms in the reactants. The reactant can be an entire molecule or a molecular fragment. For example, PNGase-F hydrolyzes the N-glycan side chains of glycoproteins and glycopeptides. To simplify this generalization, we define the reactant (substrate) of PNGase-F to be an N-glycan, which is a molecular_fragment, even though PNGase-F acts on the entire molecule. 1 A property that specifies the geometric orientation of substituents around each assymetric atom in a carbohydrate_residue. A carbohydrate_residue has several assymetric centers, and its configuration is specified by a standard identifier, such as gluco, arabino, etc. When the carbohydrate_residue has more than 4 assymetric centers, combined identifiers are used, as D-glycero-D-manno. A beta-D-glucopyranose residue b-D-Glcp beta-D-glucose CHEBI:15903 A chemical property of an entire molecule D-Man-ol D-mannitol A D-mannitol residue D-GlcNAc-ol N-acetyl-D-glucosaminitol An N-acetyl-D-glucosaminitol in the chemical context of an N-glycan An oligosaccharide derived from an N-glycan by enzymatic or chemical release from a glycoprotein/glycopeptide. The precursor of each of these oligosaccharides is an N-glycan and the residues of the N-glycan are precursor residues for the residues in the oligosaccharide. A carbohydrate residue that is classified primarily by the number of carbons in the ring A property that specifies whether the anomeric carbon of a carbohydrate_residue is involved in a glycosidic bond. If it is not, then the carbohydrate_residue is a reducing_carbohydrate_residue. a-D-Galf An alpha-D-galactofuranose residue A tyrosine residue Y Tyr A collection of interconnected atoms, but not a complete molecule A chemical property of a residue A beta-L-arabinofuranose residue b-L-Araf A sugar_structural_variation that specifies the location of nitrogen atoms that replace an oxygen in the carbohydrate_residue. A functional_group is a simple molecular fragment that has a distinct elemental composition and a distinct mode of attachment to the rest of the molecule. Functional groups typically have less than 10 atoms and are frequently represented by the uppercase letter R. Examples are the methyl group, where R = -Me = 0CH3 and the acetyl group, where R = -Ac = -COCH3. N.B. The curent version of GlycO does not suport the specification of intramolecular_link between a functional_group and another part of the molecule. That is, a functional group is merely a way of specifying that a residue, etc. contains a certain grouping of atoms. As an example, GlcNAc has an N-acetyl functional_group, but there is no need to specify an intramolecular link from the acetyl group to the nitrogen, as this is implied by the residue name GlcNAc. F A phenylalanine residue Phe A 2-deoxy-ribose residue (component of DNA). dRib A glutamine residue Q Gln D-GlcpNAc A D-N-acetyl-glucosame residue with the pyranose ring form CHEBI:17411 N-acetyl-D-glucosamine A hydrogen atom in a specific chemical context within a non-standard_residue a-L-Araf An alpha-L-arabinofuranose residue GalN A carbohydrate residue that corresponds to a galactose in which O2 is replced by a nitrogen An atom for which the chemical context is specified, e.g., C1 of an aldose is the anomeric carbon. A molecule produced or utilized by a living organism A property that specifies the stereochemistry of the anomeric carbon of a carbohydrate_residue. A covalent_bond between the anomeric carbon of a carbohydrate residue and a nitrogen atom of a nucleoside base. A carbohydrate residue with ketone at C3 1 The basic building block of a glycan (or carbohydrate, in general). A carbohydrate_residue that is classified primarily by specification of oxygens that are replaced by other atoms. These include variations such as "dideoxy", "deoxy", and "amino" that distinguish the residue from the basic residue type. For example, GlcN is common shorthand for 2-deoxy-2-amino-glucose. Here, glucose is the basic sugar type and deoxy and amino are structural variations that specify the replacement of an oxygen with a nitrogen. A nitrogen atom in a specific chemical context within an amino_acid_residue An N-glycan_derived_oligosaccharide in which the arm initiated with an alpha mannose attached to O6 of the core b-D-Manp residue contains only Man residues, while the the arm initiated with an alpha mannose attached to O3 of the core b-D-Manp residue has antennae (each containing at least one b-GlcpNAc residue). A chemical or structural property of a molecule or molecular fragment. A glycosyl transfer reaction that is catalyzed by an enzyme. Conplex N-glycans have antennae that originate with the addition of b-GlcpNAc residues to Man residues (e.g., by the action of GlcNAc transferases). A molecule containing a single nucleotide_moiety. An intramolecular link between one residue and another residue. A residue link embodies a covalent bond, which provides more detailed information regarding the link. For example, a residue_link between a b-D-Manp residue and a b-D-GlcpNAc residue can embody a glycosidic_covalent_bond between C1 of the b-D-Manp residue and O4 of the b-D-GlcpNAc residue. A nitrogen atom in a specific chemical context within a carbohydrate_residue N An O-glycan is an oligosaccharyl moiety that is linked to an oxygen atom in a serine, threonine, hydroxylysine, or hydroxyproline residue in a glycpeptide or glycoprotein. A molecular fragment that contains a deoxy ribose residue and a nucleoside_base residue. Leu L A leucine residue A sugar_structural_variation that specifies the identity and location of functional groups (such as N-acetyl groups) that are considered integral parts of the carbohydrate-residue. For example, a GlcNAc residue has a sugar_functional_group_substitution_variation that is _2-N-acetyl An alpha-N-acetyl-alpha-D-glucosamine residue in the chemical context of an N-glycan a-D-GlcpNAc A carbohydrate residue with 6 main-chain carbon atoms, C1 as the anomeric carbon, and oxygen atom O6 missing An alpha-D-glucopyranose residue in the chemical context of an N-glycan a-D-Glcp A chemical property of a molecular fragment 8 A carbohydrate residue with 8 main-chain carbon atoms An L-Fuc residue with the pyranose ring form L-Fucp CHEBI:18287 H A hydrogen atom in a specific chemical context within a carbohydrate_residue D-Glcf A D-glucofuranose residue A carbohydrate residue with ketone at C2 that is not glycosidically linked to another moiety A sugar_structural_variation that specifies the location of carbonyl carbons in the main chain of the carbohydrate_residue. galactitol 0 Galol Gal-ol A galactitol residue - galactitol is meso, so D and L have no significance for this molecule. b-D-Manp A beta-D-mannopyranose residue in the chemical context of an N-glycan Glu A glutamic acid residue E A protein that binds specifically to a carbohydrate_moiety. Lectins are distinct from antibodies, some of which may bind to carbohydrate epitopes. a glycan moiety is a glycan that is part of a glycoconjugate, which also has a non-carbohydrate moiety 2 1 D-GalN A GalN residue with the absolute configuration D An N-acetyl-neuraminic acid residue NeuAc NeuAc N-acetyl 5-N-acetyl An N-glycan_derived_oligosaccharide that has ONLY mannosyl residues attached to the core. An alpha-N-acetyl-neuraminic acid residue (pyranose) a-NeuAc An L-serine residue Ser S A lectin produced by an animal species A beta-D-mannopyranose residue CHEBI:28563 b-D-Manp An aspartic acid residue Asp D NeuGc NeuGc N-glycolyl An N-glycolyl-neuraminic acid residue 5-N-glycolyl N-glycolyl A covalent_bond between the anomeric carbon of a carbohydrate residue and an oxygen another carbohydrate_residue. N A nitrogen atom in a specific chemical context within a nucleoside_base_residue aldonic aldonic A carbohydrate residue in which C1 is oxidized to a carboxylic acid Achemical reaction that is catalyzed by an enzyme. A glycosylated oligopeptide (in which the peptide contains only a few amino_acid_residues). 6 CHEBI:24590 A carbohydrate residue with 6 main-chain carbon atoms The basic building block of a peptide or protein. A carbon atom in a specific chemical context within a nucleoside_base_residue C b-D-Galf A beta-D-galactofuranose residue A D-glucose residue A carbohydrate residue in the chemical context of a nucleoside or nucleotide. 6-deoxy deoxy A carbohydrate residue in which oxygen atom O6 is missing A carbohydrate residue in the chemical context of a monoglycosyl_moiety A molecular fragment that is lipid in nature. An example is dolichol, a lipid that is part of the glycolipid precursors of N-glycans. A collection of atoms that constitute a complete molecule. D-Xylose CHEBI:15936 A D-xylopyranose residue D-Xylp A molecular_property of an enzyme, this specifies the chemical mechanism by which the enzyme operates. This can be very simple (as in inverting and retaining mechanisms). A sulfur atom in a specific chemical context within an amino_acid_residue val V A valine residue N An asparagine residue The nitrogen atom attached to C4 of an amino acid. This is the nitrogen atom (in asparagine residues) that N-glycans are linked to. The carbonyl oxygen of the C1 carboxyl group of an amino acid The alpha amino atom of an amino_acid_residue Asn This is the alpha proton of an amino acid An N-glycan_derived_oligosaccharide that has antennae that originate with the addition of b-GlcpNAc residues to Man residues (e.g., by the action of GlcNAc transferases). 9 A carbohydrate residue with 9 main-chain carbon atoms A xylose residue Xyl Xyl xylo A 3-deoxy-2-octulosonic acid residue, commonly known as KDO A carbohydrate residue in which oxygen atom O3 is missing The anomeric carbon of the reducing form of the sugar is a ketone keto 2-keto A carbohydrate residue with ketone at C2 A carbohydrate residue in which two oxygen atoms are missing dideoxy general specification of a dideoxy sugar wthout specifying the deoxy carbons dideoxy A glucosaminitol residue, i.e., a residue corresponding to a glucitol structure with O2 replaced by a nitrogen glucosaminitol GlcN-ol A carbohydrate residue in the chemical context of the glycan portion of anO-glycan. This includes all carbohydrate residues in O-glycans and oligosaccharides released by cleavage of O-glycans A atom of the chemical element sulfur (atomic number 16). A carbohydrate residue that has a nitrogen atom attached to C2 amino 2-amino A polyatomic molecular fragment that is larger than a residue. An example is an N-glycan, which (1) is a fragment of a glycoprotein and (2) is composed of carbohydrate_residues. An L-galactose residue A fructose residue A molecular fragment that consists of a deoxy ribose residue, a nucleoside_base residue, and at least one linked_phosphate_residue. A protein generated by the immune system of an organism to specifically bind to an epitope. A carbohydrate residue defined primarily by its chemical context in a glycan of a specific type A 3-deoxy-D-manno-2-octulosonic acid residue, commonly known as KDO A carbohydrate residue with ketone that is not glycosidically linked to another moiety A residue consisting of a cyclic, aromatic base (i.e., purine or pyrimidine) that is a component of a nucleoside A carbohydrate residue with ketone at C2 and 9 carbons in the main chain 0 A residue is a subunit of a polymer. For most biopolymers, hydrolysis breaks bonds between the residues to generate a collection of small molecules, such as amino acids, nucleotides, or monosaccharides, which are called residues in the context of the polymer which they constitute. 0 0 0 A carbon atom in a specific chemical context within a carbohydrate_residue C A proline residue Pro P A protein that catalyzes the hydrolysis of a glycosidic bond. A beta-D-mannopyranosyl residue in the context of a monoglycosyl_moiety A covalent_bond between the anomeric carbon of a carbohydrate residue and an oxygen atom of a phosphate residue. A beta-D-glucopyranosyl residue in the context of a monoglycosyl_moiety A molecular fragment that contains a ribose residue and a nucleoside_base residue. A covalent_bond between two atoms within a single residue, such as the bond between O2 and C2 of a Glc residue. A molecular fragment that consists of amino acids that are covalently lined to each other by peptide bonds in a linear array. A carbohydrate residue with ketone at C2, 9 carbons in the main chain, and missing O3 and O5 An alpha-D-galactopyranose residue in the chemical context of an N-glycan a-D-Galp An molecule consisting ofmany carbohydrate_residues. If the polymer is attached to a protein or lipid, it should be classified as a proteoglycan or glycolipid. W Trp A tryptophan reside A hydrogen atom in a specific chemical context within an amino_acid_residue amino 5-amino A carbohydrate residue that has a nitrogen atom attached to C5 D-Xyl A D-xylose residue One of the residues in a larger structure can often be considered the root of a tree that describes the larger structure. Associates a functional_group to a larger structure that contains this functional group. For example, GlcNAc contains_functional_group N-acetyl. In contrast, a GlcNAc MAY also be connected to a sulfate (non-standard_residue) via an intramolecular_link. The sulfate non-standard_residue is not part of the GlcNAc residue itself. When an N-glycan, O-glycan, etc is detached from a glycoconjugate, an oligosaccharide is released A representation of the combined geometric orientation of all the assymetric atoms in the sugar residue, except for the anomeric carbon. Associates a non-standard_residue with a structure that contains it. This property is distinct from has_functional_group, as in structure that has_non-standard_residue, the connection between the non-standard_residue and other components of the structure must be specified by an intramolecular_link does not necessarily imply that the residue changed in a reaction The mass of one copy of the chemical entity (in Daltons) when all atoms are present as the most abundant isotope (i.e., 1H, 12C, 16O, etc.) The monoisotopic mass of methane (CH4) is 16.03 The mass of one copy of the chemical entity (in Daltons) calculated using the natural-abundance weight-averaged mass of each atom. The chemcial mass of methane (CH4) is 16.04 Da. A glycosyl residue is added to the acceptor substrate by transfer of a carbohydrate residue from the donor substrate (usually a nucleotide sugar) to form the product (a glycan or glycoside). The glycosyl residue here is defined within the context of the product (acceptor plus glycosyl residue). Each residue has a name that corresponds to the name of the monosaccharide to which the residue is converted upon hydrolysis of the glysan. Number of bonds connecting the functional group to the rest of the molecule. For example, 1 bond connects a methyl group to the molecule (-Me), while 2 bonds connect an oxo-group to the molecule (=O). A one-letter representation (often italicized) of the number of atoms in the sugar residue ring. The letter p represents a pyranoid (6 membered) ring and the letter f represents a furanoid (5 membered) ring. a-D-Manp CHEBI:28729 Man This link embodies a link between the N-glycan_a-D-Manp_7 residue and the N-glycan_core_b-D-Manp residue. link from N-glycan_a-D-Manp_7 to N-glycan_core_b-D-Manp CHEBI:28563 Man b-D-Manp CHEBI:28009 GlcNAc b-D-GlcpNAc Man a-D-Manp CHEBI:28729 link from N-glycan_a-D-Manp_4 to N-glycan_core_b-D-Manp This link embodies a link between the N-glycan_a-D-Manp_4 residue and the N-glycan_core_b-D-Manp residue. GlcNAc CHEBI:28009 b-D-GlcpNAc [][D-GlcNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(6+1)][b-D-GlcpNAc]{}}}} G06558 This link embodies a link between the N-glycan_core_b-D-Manp residue and the N-glycan_reducing_core_D-GlcNAc_B residue. link from N-glycan_core_b-D-Manp to N-glycan_reducing_core_D-GlcNAc_B GlcNAc D-GlcNAc-ol D-GlcNAc b-D-GlcpNAc GlcNAc CHEBI:28009 link from N-glycan_b-D-GlcpNAc_9 to N-glycan_a-D-Manp_4 This link embodies a link between the N-glycan_b-D-GlcpNAc_9 residue and the N-glycan_a-D-Manp_4 residue. link from N-glycan_b-D-GlcpNAc_12 to N-glycan_a-D-Manp_4 This link embodies a link between the N-glycan_b-D-GlcpNAc_12 residue and the N-glycan_a-D-Manp_4 residue. GlcNAc N-glycan_core_a-D-GlcpNAc_A N-glycan_precursor_moiety_G00002 link from N-glycan_core_b-D-GlcpNAc_B to N-glycan_core_a-D-GlcpNAc_A This link embodies a link between the N-glycan_core_b-D-GlcpNAc_B residue and the N-glycan_core_a-D-GlcpNAc_A residue. dolichol_pyrophosphate_moiety At this time, the only dolichol atom specified is O1 . N-Acetyl-D-glucosaminyldiphosphodolichol N-glycan_precursor_moiety_G00001 A moiety consisting of a single a-D-GlcpNAc residue Rib C00105 G10610 UDP-GlcNAc UDP This link embodies a link between the N-glycan_b-D-Galp_56 residue and the N-glycan_b-D-GlcpNAc_10 residue. Gal b-D-Galp CHEBI:27667 b-D-GlcpNAc GlcNAc link from N-glycan_b-D-Galp_56 to N-glycan_b-D-GlcpNAc_10 link from N-glycan_core_b-D-Manp to N-glycan_core_b-D-GlcpNAc_B This link embodies a link between the N-glycan_core_b-D-Manp residue and the N-glycan_core_b-D-GlcpNAc_B residue. This link embodies a link between the N-glycan_b-D-GlcpNAc_10 residue and the N-glycan_a-D-Manp_4 residue. link from N-glycan_b-D-GlcpNAc_10 to N-glycan_a-D-Manp_4 GlcNAc GlcNAc D-GlcNAc GlcNAc-ol GlcNAc-ol CHEBI:28009 b-D-GlcpNAc G10812 [][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}} This link embodies a link between the N-glycan_core_b-D-GlcpNAc_B residue and the N-glycan_core_b-D-GlcpNAc_A residue. link from N-glycan_core_b-D-GlcpNAc_B to N-glycan_core_b-D-GlcpNAc_A link from N-glycan_core_b-D-GlcpNAc_B to N-glycan_D-GlcNAc-ol_A This link embodies a link between the N-glycan_core_b-D-GlcpNAc_B residue and the N-glycan_D-GlcNAc-ol_A residue. [][D-GlcNAc-ol]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}} This link embodies a link between the N-glycan_b-D-GlcpNAc_14 residue and the N-glycan_a-D-Manp_7 residue. link from N-glycan_b-D-GlcpNAc_14 to N-glycan_a-D-Manp_7 b-D-GlcpNAc GlcNAc CHEBI:28009 G04303 This link embodies a link between the N-glycan_b-D-GalpNAc_22 residue and the N-glycan_b-D-GlcpNAc_12 residue. b-D-GalpNAc CHEBI:28497 GalNAc link from N-glycan_b-D-GalpNAc_22 to N-glycan_b-D-GlcpNAc_12 CHEBI:27667 b-D-Galp Gal GlcNAc b-D-GlcpNAc CHEBI:28009 CHEBI:27667 b-D-Galp Gal This link embodies a link between the N-glycan_b-D-GlcpNAc_49 residue and the N-glycan_b-D-Galp_28 residue. link from N-glycan_b-D-GlcpNAc_49 to N-glycan_b-D-Galp_28 This link embodies a link between the N-glycan_b-D-Galp_28 residue and the N-glycan_b-D-GlcpNAc_14 residue. link from N-glycan_b-D-Galp_28 to N-glycan_b-D-GlcpNAc_14 link from N-glycan_b-D-Galp_54 to N-glycan_b-D-GlcpNAc_49 This link embodies a link between the N-glycan_b-D-Galp_54 residue and the N-glycan_b-D-GlcpNAc_49 residue. b-D-GlcpNAc GlcNAc CHEBI:28009 NeuAc CHEBI:17012 a-Neu5Ac link from N-glycan_a-Neu5Ac_41 to N-glycan_b-D-Galp_24 b-D-Galp Gal CHEBI:27667 This link embodies a link between the N-glycan_a-Neu5Ac_41 residue and the N-glycan_b-D-Galp_24 residue. G03765 link from N-glycan_b-D-Galp_24 to N-glycan_b-D-GlcpNAc_13 This link embodies a link between the N-glycan_b-D-Galp_24 residue and the N-glycan_b-D-GlcpNAc_13 residue. [][D-GlcNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}} b-D-Galp Gal CHEBI:27667 This link embodies a link between the N-glycan_b-D-Galp_21 residue and the N-glycan_b-D-GlcpNAc_12 residue. link from N-glycan_b-D-Galp_21 to N-glycan_b-D-GlcpNAc_12 This link embodies a link between the N-glycan_core_b-D-GlcpNAc_B residue and the N-glycan_reducing_core_D-GlcNAc_A residue. link from N-glycan_core_b-D-GlcpNAc_B to N-glycan_reducing_core_D-GlcNAc_A link from N-glycan_b-D-GlcpNAc_13 to N-glycan_a-D-Manp_7 This link embodies a link between the N-glycan_b-D-GlcpNAc_13 residue and the N-glycan_a-D-Manp_7 residue. NeuGc a-Neu5Gc This link embodies a link between the N-glycan_b-D-GalpNAc_29 residue and the N-glycan_b-D-GlcpNAc_14 residue. link from N-glycan_b-D-GalpNAc_29 to N-glycan_b-D-GlcpNAc_14 GalNAc b-D-GalpNAc CHEBI:28497 This link embodies a link between the N-glycan_a-Neu5Gc_34 residue and the N-glycan_b-D-Galp_21 residue. link from N-glycan_a-Neu5Gc_34 to N-glycan_b-D-Galp_21 a-D-Glcp Glc a-D-Manp Man CHEBI:28729 link from N-glycan_a-D-Glcp_51 to N-glycan_a-D-Manp_30 a-D-Manp CHEBI:28729 Man This link embodies a link between the N-glycan_a-D-Glcp_51 residue and the N-glycan_a-D-Manp_30 residue. G05893 This link embodies a link between the N-glycan_a-D-Manp_15 residue and the N-glycan_a-D-Manp_7 residue. link from N-glycan_a-D-Manp_15 to N-glycan_a-D-Manp_7 link from N-glycan_a-D-Manp_30 to N-glycan_a-D-Manp_15 This link embodies a link between the N-glycan_a-D-Manp_30 residue and the N-glycan_a-D-Manp_15 residue. [][D-GlcNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(3+1)][a-D-Glcp]{}}}}}}} CHEBI:28729 Man a-D-Manp a-D-Manp CHEBI:28729 Man This link embodies a link between the N-glycan_a-D-Manp_16 residue and the N-glycan_a-D-Manp_8 residue. link from N-glycan_a-D-Manp_16 to N-glycan_a-D-Manp_8 a-D-Manp Man Man a-D-Manp CHEBI:28729 link from N-glycan_a-D-Manp_19 to N-glycan_a-D-Manp_11 This link embodies a link between the N-glycan_a-D-Manp_19 residue and the N-glycan_a-D-Manp_11 residue. link from N-glycan_a-D-Manp_8 to N-glycan_a-D-Manp_4 This link embodies a link between the N-glycan_a-D-Manp_8 residue and the N-glycan_a-D-Manp_4 residue. This link embodies a link between the N-glycan_a-D-Manp_11 residue and the N-glycan_a-D-Manp_4 residue. link from N-glycan_a-D-Manp_11 to N-glycan_a-D-Manp_4 a-Neu5Ac NeuAc CHEBI:17012 G10702 link from N-glycan_a-Neu5Ac_47 to N-glycan_b-D-Galp_28 This link embodies a link between the N-glycan_a-Neu5Ac_47 residue and the N-glycan_b-D-Galp_28 residue. a-Neu5Ac CHEBI:17012 NeuAc [][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}}}} link from N-glycan_a-Neu5Ac_36 to N-glycan_b-D-Galp_21 This link embodies a link between the N-glycan_a-Neu5Ac_36 residue and the N-glycan_b-D-Galp_21 residue. hydroxymethyl CHEBI:28009 b-D-GlcpNAc GlcNAc CHEBI:27667 Gal b-D-Galp This link embodies a link between the N-glycan_b-D-Galp_53 residue and the N-glycan_b-D-GlcpNAc_39 residue. link from N-glycan_b-D-Galp_53 to N-glycan_b-D-GlcpNAc_39 GlcNAc CHEBI:28009 b-D-GlcpNAc link from N-glycan_b-D-Galp_52 to N-glycan_b-D-GlcpNAc_33 This link embodies a link between the N-glycan_b-D-Galp_52 residue and the N-glycan_b-D-GlcpNAc_33 residue. b-D-Galp Gal CHEBI:27667 [][Methyl]{[(1+1)][b-D-Glcp]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}}} Gal b-D-Galp CHEBI:27667 link from N-glycan_b-D-GlcpNAc_39 to N-glycan_b-D-Galp_21 This link embodies a link between the N-glycan_b-D-GlcpNAc_39 residue and the N-glycan_b-D-Galp_21 residue. This link embodies a link between the N-glycan_b-D-GlcpNAc_33 residue and the N-glycan_b-D-Galp_17 residue. link from N-glycan_b-D-GlcpNAc_33 to N-glycan_b-D-Galp_17 link from N-glycan_b-D-Galp_17 to N-glycan_b-D-GlcpNAc_9 This link embodies a link between the N-glycan_b-D-Galp_17 residue and the N-glycan_b-D-GlcpNAc_9 residue. G04190 [][D-GlcNAc-ol]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}} G02757 CHEBI:17012 a-Neu5Ac a-Neu5Gc This link embodies a link between the N-glycan_a-Neu5Ac_46 residue and the N-glycan_b-D-Galp_28 residue. link from N-glycan_a-Neu5Ac_46 to N-glycan_b-D-Galp_28 link from N-glycan_core_b-D-Manp to N-glycan_D-GlcNAc-ol_B This link embodies a link between the N-glycan_core_b-D-Manp residue and the N-glycan_D-GlcNAc-ol_B residue. G01863 [][D-GlcNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(3+1)][a-D-Glcp]{}}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}} O-methyl CHEBI:28009 GlcNAc b-D-GlcpNAc link from N-glycan_b-D-GlcpNAc_5 to N-glycan_core_b-D-Manp This link embodies a link between the N-glycan_b-D-GlcpNAc_5 residue and the N-glycan_core_b-D-Manp residue. G04171 [][D-GlcNAc-ol]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-D-GlcpNAc]{}}}}} [][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}} G10643 UMP C00105 G04148 [][D-GlcNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}} This link embodies a link between the N-glycan_a-D-Galp_60 residue and the N-glycan_b-D-Galp_24 residue. link from N-glycan_a-D-Galp_60 to N-glycan_b-D-Galp_24 Gal a-D-Galp CHEBI:28061 G04178 [][D-GlcNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}} G04336 [][Thr]{[(2+1)][Gly]{[(2+1)][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}}}} G04567 [][D-GlcNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}} G02043 [][D-GlcNAc-ol]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}} G04502 [][D-Glc3Me]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}} b-D-Galp CHEBI:27667 Gal G10740 [][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{}}}}} link from N-glycan_core_b-D-GlcpNAc_B to N-glycan_reductively_aminated_D-GlcNAc-ol_A This link embodies a link between the N-glycan_core_b-D-GlcpNAc_B residue and the N-glycan_reductively_aminated_D-GlcNAc-ol_A residue. G05728 [][2-aminopyridine]{[(2+1)][D-GlcNAc-ol]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{}}}}} [][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}} G10694 CHEBI:18287 a-L-Fucp Fuc G10721 [][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}} G04857 [][D-GlcNAc-ol]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{}}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}} G02982 [][D-GlcNAc-ol]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(6+1)][b-D-GlcpNAc]{}}}}} G05405 [][<rest]{[(?+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}} G10824 [][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}} [][D-GlcNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}} G04199 CHEBI:28061 Gal a-D-Galp link from N-glycan_a-D-Galp_61 to N-glycan_b-D-Galp_28 This link embodies a link between the N-glycan_a-D-Galp_61 residue and the N-glycan_b-D-Galp_28 residue. CHEBI:28061 Gal N-glycan_a-D-Galp_61 [][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}}} This link embodies a link between the N-glycan_a-Neu5Ac_31 residue and the N-glycan_b-D-Galp_17 residue. CHEBI:17012 NeuAc a-Neu5Ac link from N-glycan_a-Neu5Ac_31 to N-glycan_b-D-Galp_17 G04046 [][Thr]{[(2+1)][Gly]{[(2+1)][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}}}} CHEBI:17012 NeuAc a-Neu5Ac link from N-glycan_a-Neu5Ac_40 to N-glycan_b-D-Galp_24 This link embodies a link between the N-glycan_a-Neu5Ac_40 residue and the N-glycan_b-D-Galp_24 residue. G04941 [][D-GlcpNAc]{[(4+1)][b-D-4-deoxy-lyxHexp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}} G01366 G00369 [][D-GlcNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}} [][D-GlcNAc-ol]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}} G03834 G11958 [][Dansyl]{[(1+2)][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{}}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}} [][2-aminopyridine]{[(2+1)][D-GlcNAc-ol]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{}}}[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{}}}}}}}} G03925 [][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}} G10819 [][D-GlcNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}} G02243 G10801 [][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{}}}}} This link embodies a link between the N-glycan_b-D-Galp_26 residue and the N-glycan_b-D-GlcpNAc_13 residue. link from N-glycan_b-D-Galp_26 to N-glycan_b-D-GlcpNAc_13 [][Thr]{[(2+1)][Tyr]{[(2+1)][Asn]{[(2+1)][Thr]{[(2+1)][Thr]{[(2+1)][Thr]{[(2+1)][Ser]{[(2+1)][Ala]{}}}}}[(4+1)][b-D-Glcp]{[(3+1)][b-D-Galp]{}}}}} G12091 b-D-Xylp Xyl [][2-aminopyridine]{[(2+1)][D-GlcNAc-ol]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}} G00890 link from N-glycan_b-D-Xylp_6 to N-glycan_core_b-D-Manp This link embodies a link between the N-glycan_b-D-Xylp_6 residue and the N-glycan_core_b-D-Manp residue. link from N-glycan_a-D-Galp_58 to N-glycan_b-D-Galp_56 Gal CHEBI:28061 a-D-Galp This link embodies a link between the N-glycan_a-D-Galp_58 residue and the N-glycan_b-D-Galp_56 residue. [][D-GlcNAc-ol]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}} G03719 [][D-6-deoxy-Glc]{[(?+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}} G04503 [][D-GlcNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}} G00595 G03265 [][D-GlcNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{}}}} G07842 [][D-GlcNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(4+1)][b-D-GlcpNAc]{}}}} GDP GDP-Man A moiety consisting of a single a-D-Manp residue G10526 [][dolichol-PP]{[(0+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}} G01934 [][D-GlcNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(6+1)][b-D-GlcpNAc]{}}}} G10618 A moiety consisting of a single b-D-Glcp residue [][D-GlcNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{}}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(6+1)][a-D-Manp]{}}}}} G04895 [][D-GlcNAc-ol]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}}