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., 2001 ▶). (b) Superfluous LINK records can be found when nonlinked atoms are rather close in space (PDB entry 1apy; Oinonen et al., 1995 ▶). (c) In entry 1pxx (Rowlinson et al., 2003 ▶), 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., 2007 ▶). (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, 2008 ▶).