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![[Figure 5]](ir5021fig5mag.jpg)
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Figure 5
Description of the covalent linkage of lysine (LYS) and pyridoxal phosphate (PLP) using AceDRG. (a) Chemical diagrams of the individual LYS and PLP components (from the CCP4-ML) and (b) the linked composite compound, in which the covalent linkage is depicted as a dotted line (created using ChemDraw Professional 17.1). (c) Comparison of a deposited 1.8 Å resolution model (PDB entry 6ndn; J. F. Scortecci, J. Brandao-Neto, H. M. Pereira & O. H. Thiemann, unpublished work; purple) and the model re-refined with REFMAC5 using an AceDRG link dictionary (green), focusing on LYS-A226 and PLP-A501, displayed using Coot. Interatomic distances and dotted lines correspond to the covalent linkage. The 2mFo − DFc map corresponding to the re-refined model is shown as a grey mesh. Transparent surfaces surrounding atoms in the linked complex highlight the atoms involved in link-dictionary restraints, corresponding to (d) changes to bond/angle restraints (red surface), (e) torsion-angle restraints (green), (f) planar restraints that are removed (blue) and (g) planar restraints that are added (gold) due to the covalent linkage. Note that the O4A atom deleted from PLP (and thus not shown) was involved in the removed planar restraint. H atoms were modelled in riding positions using REFMAC5. |
![[Figure 5]](ir5021fig5.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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