N-glycan core structure (with frequent additions) and an example of erroneous PDB data. (a) Carbohydrate chains that are linked to an Asn side chain (N-glycans) comprise a well defined core structure of two β-D-GlcpNAc, one β-D-Manp and two α-D-Manp residues (`GlcNAc2Man3 core'), displayed in bold letters. At positions 3 and/or 6 of the proximal β-D-GlcpNAc, α-L-Fucp residues can be added (`core fucosylation'). Some residues are only present in certain species. For example, the β-D-Xylp and α-D-Araf residues that are linked to position 2 of β-D-Manp are found, for example, in insects, molluscs or plants but not in mammals. The core structure can be further extended (mainly by D-GlcpNAc, D-Galp, D-GalpNAc, D-Manp, D-Neup5Ac, L-Fucp or D-Glcp) at the α-D-Manp residues in a species-specific manner. (b) Primary structure of an N-glycan chain from PDB entry 3d12
(Xu et al., 2008), in which none of the residues is known at its position in N-glycans to date and which probably is based on misinterpretation of the electron density.