Figure 4

Structural refinement. (A) Spatial similarities of the VR and reductase domain binding sites. Vestitone (white line ball-and-stick) is superimposed on the R domain using the VR-vestitone docking coordinates. Energetically optimal conformations for Alamethicin (cyan, ball-and-stick), Trichotoxin (green, ball-and-stick), Antiamoebin I (magenta, ball-and-stick), Chrysopermin (yellow, ball-and-stick), Gramicidin (red, ball-and-stick) and NADPH (orange, ball-and-stick) predicted by MOE-Dock 2008.10 are pictured. For a given ligand, the result of each docking simulation is represented by a single chemical structure. (B) The putative substrate-binding pockets in the modeled structure of the R domain. Some amino acid residues in the binding pockets of the R domain are labeled and shown as a brown colored stick model. (C) RMSD of the R domain backbone atoms during 2-ns MD simulation.