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Figure 3 | BMC Structural Biology

Figure 3

From: Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases

Figure 3

Evaluation of the reductase domain model. (A) The superposition of the modeled R domain (colored in cyan) with the crystal structure of VR (colored in yellow). The reductase characterizes the SYK triad for catalytic function (left). The modeled structure containing Ser142, Tyr176 and Lys180 is highlighted in cyan. The red residues are the corresponding residues of VR (right). (B) 3D structure profile for the modeled R domain. The structures of the template (2p4h) and the R domain are shown in green and blue color, respectively. (C) The Ramachandran plot of modeled reductase refined by MD simulation. A total of 270 residues (84.6%) fall in the most favored regions (cyan), while 38 residues (11.8%) fall in additional allowed regions (orange) and 12 residues (3.7%) fall in the additional allowed regions (pale orange). No residues fall in the additionally allowed region.

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