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Figure 4
Conformer generation, ligand fitting and link creation, exemplified using pyridoxal 5′-phosphate (monomer code: PLP). (a) displays an unmodelled blob in the density of a structure solved using data extending to 1.6 Å resolution (PDB entry 1ajs; Rhee et al., 1997BB43) after manually removing the ligand from the deposited model. When importing the ligand, the model will not necessarily be in the correct pose or conformation (b). Automatic conformer generation and ligand fitting results in a more reasonable pose and conformation for the coenzyme (c). Creation of a link record, describing the bond between the N atom in the side chain of Lys258 and a C atom in PLP, can be achieved by opening the Lys and PLP in JLigand (d). The O atom (O4A) in PLP can then be removed and the double-bond link created between the lysine N atom (NZ) and the C atom (C4A) in PLP (e). The model is shown following subsequent refinement by REFMAC5 (f).

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ISSN: 2059-7983
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