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Figure 8
Examples of errors in carbohydrate chains in the PDB. (a) Missing LINK records can result in too large distances between individual residues (PDB entry 1eqh ; Selinsky et al., 2001BB113). (b) Superfluous LINK records can be found when nonlinked atoms are rather close in space (PDB entry 1apy ; Oinonen et al., 1995BB93). (c) In entry 1pxx (Rowlinson et al., 2003BB106), the C1 atom is missing, although all three surrounding atoms are resolved in the three-dimensional structure. (d) Superfluous atoms (cyan) are sometimes found within glycosidic linkages (Dellisanti et al., 2007BB22). (e) When individual unconnected residues are arranged in a way that is usually found in N-glycan chains, they probably should be linked to each other, which would result in a deletion of the O1 atoms (PDB entry 3d2u ; Yang & Bjorkman, 2008BB141).

Journal logoBIOLOGICAL
ISSN: 1399-0047
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