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Figure 8
Comparison of the thioether bridge in a PDB annotated model (protein chain A and N3 inhibitor chain D in PDB entry 2q6f; Xue et al., 2008BB58) and the same model after re-refinement with REFMAC5 using a link record and an AceDRG dictionary (figure created using Coot; Emsley et al., 2010BB14). (a) The relevant link record was not present in the annotated model; this is reflected in the purple/red Coot dots that represent outlier clashes between atoms involved in the thioether bridge; this representation is similar to that produced via PROBE (Word et al., 1999BB56) all-atom contact analysis in MolProbity (Chen et al., 2010BB8). (b) After re-refinement using an AceDRG dictionary, there are no clashes. Visible residues in the N3 inhibitor are labelled, as is the interacting CYS-143 residue. Atoms CYS-143[SG] and PJE-5[C20] involved in the covalent linkage (dashed line) are labelled in the re-refined model (b); for visual clarity these are omitted from (a). The atom PJE-5[C21] is also identified; it should be noted that the C20–C21 bond in PJE changes order from double to single when the covalent linkage is modelled correctly.

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ISSN: 2059-7983
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