A atom of the chemical element oxygen (atomic number 8). 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.) 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. alpha-D-galactose CHEBI:28061 a-D-Galp An alpha-D-galactopyrano residue a &945; D-Manp CHEBI:16024 A D-mannopyrano residue b-D-Xylp CHEBI:28161 b &946; A 6-deoxy-aldoHex_residue with galacto configuration Fuc Fuc galacto A monoglycosyl moiety contains a single carbohydrate_residue. This moiety is glycosidically linked to another (presumably non-carboohydrate) moiety. 1 1 A glycine residue Gly G beta-D-galactose A beta-D-galactopyrano residue CHEBI:27667 b-D-Galp A D-galactose residue D The anomeric carbon of the reducing form of the sugar is a aldehyde aldo aldo Havig a six membered ring, indicated by an italicized p p N-acetyl gluco GlcNAc 1 N-glycan_core_a-D-GlcpNAc_A 1 A carbohydrate residue with an aldehyde at C1 and a five-membered ring UDP-GlcNAc 5 An isoleucine residue I Ile N-acetyl-glucosaminyl_transferase_V A atom of the chemical element phosphorous (atomic number 15). L-Araf An L-arabinofurano residue N-acetyl-alpha-D-glucosamine a-D-GlcpNAc An N-acetyl-alpha-D-glucosamine residue with the anomeric configuration alpha A carbohydrate residue with 6 main-chain carbon atoms, C1 as the anomeric carbon, and no oxygen atoms are missing Thr An L-trheonine residue T 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 A beta-N-acetyl-neuraminic acid residue UDP-Gal 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. manno A mannose residue Man The word peptide commonly signifies an oligopeptide, but it can be used to signify a polypeptide (protein) 2 1 a free glycan is a carbohydrate that is not part of a glycocongugate A residue with the absolute configuration D L-Ara a-L-Fucp An L-Fucp residue with the alpha anomeric configuration An L-galactopyrano residue L-Galp 4 A D-galactofurano 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 also called a polypeptide An L-proline residue P Pro CHEBI:24590 1 A carbohydrate residue with an aldehyde at C1 N-acetyl-beta-D-galactosamine A beta-N-acetyl-alpha-D-galactosamine residue in the chemical context of an N-glycan CHEBI:28497 b-D-GalpNAc A carbohydrate residue that corresponds to a glucose in which O2 is replced by a nitrogen GlcN L-Galf An L-galactofurano residue A glycosylated polypeptide A polysaccaride attached to a peptide CHEBI:28518 a-D-Xylp An acidic amino acid residue 3-deoxy deoxy 5-deoxy deoxy 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. 7 D-Galp D-galactose CHEBI:17118 A D-galactopyrano residue A GlcN residue with the absolute configuration D D-GlcN An atom in a specific chemical context within a carbohydrate_residue C 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 cyclic conflicts, sugar residues are not themselves defined as carbohydrate moieties, although the carbohydrate moiety can contain exactly one sugar residue. CHEBI:17925 alpha-D-glucose a-D-Glcp An alpha-D-glucopyrano residue An alanine residue A Ala 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 The basic building block of a DNA or RNA molecule A glycosylated oligopeptide A (usually highly reactive) atomic or molecular entity that has unpaired electrons in a valence shell. 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. D-GalNAc A D-galactosame residue with an N-acetyl substituent N-acetyl 2-N-acetyl GalNAc A carbohydrate residue in which oxygen atom O2 is missing deoxy 2-deoxy A carbohydrate residue with 6 main-chain carbon atoms, C1 as the anomeric carbon, and oxygen atom O6 missing An alpha-L-galactofurano 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). . b-D-Xylp The smallest piece of a chemical element, e.g., a carbon atom. A cysteine residue Cys C A carbohydrate residue with an aldehyde at C1 and six main chain carbon atoms CHEBI:33917 water The basic building block of DNA A glucosaminitol residue with the absolute configuration D D-glucosaminitol D-GlcN-ol An aromatic amino acid residue An alpha-D-mannopyrano 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 The oveall "handedness" of a chemical entity, 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 "sugar_residue". The "sugar_configuration" subsumes the absolute configuration (e.g., "D-gluco" or "D-glycero-D-manno") but the absolute_configuration is included for generality. A galactose residue Gal CHEBI:18287 An a-L-Fucp residue in he context of an N-glycan a-L-Fucp 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). His H A histidine residue A sulfur-containing amino acid residue a-D-Manp An alpha-D-mannopyrano residue CHEBI:28729 S Ser A serine residue An alditol residue with 6 main chain carbons Any biomolecule that has amiino acids connected by peptide bonds 1 1 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 GDP-Man A carbohydrate residue with an aldehyde at C1 and five main chain carbon atoms A beta-D-galactopyrano residue in the chemical context of an N-glycan CHEBI:27667 beta-D-galactose b-D-Galp A atom of the chemical element carbon (atomic number 6). a-NeuNAc CHEBI:17012 a-Neu5Ac a-Neup5Ac A atom of the chemical element hydrogen (atomic number 1). D-Glcp CHEBI:17634 D-glucose A D-glucopyrano residue A basic amino acid residue Thr T A threonine residue N-acetyl-D-glucosaminitol D-GlcNAc-ol A D-glucosaminitol residue with an N-acetyl substituent GlcNAc-ol D-GlcNAc GlcNAc A D-glucosame residue with an N-acetyl substituent A atom of the chemical element nitrogen (atomic number 7). 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". 2 D-glycero-D-galacto A neuraminic acid residue A lipid-linked_N-glycan_precursor 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 methionine residue M Met A carbohydrate residue with no aldehyde or ketone. 0 alditolic alditolic R An arginine residue Arg A beta-L-galactopyrano residue b-L-Galp A non-polar amino acid residue (e.g., valine, leucine) An beta-N-glycolyl-neuraminic acid residue Man-ol mannitol A mannitol residue Manol A N-cyclic amino acid residue (e.g., prolne) b-D-GlcpNAc CHEBI:28009 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 Glc A glucose residue Lys