Figure 3
The structure of binding mode 22. Panel A: The C5aR backbone is shown as a thin tan tube. The first 7 residues are omitted as in the Nikiforovich model [25]; the Cα atom of the 8th residue is depicted as a vdW sphere. Protein segments in contact with PMX53 are indicated in the following colors: 113–121 (H3) in green, 164–172 (H4) in orange, 188–199 (EC2) in black, 202–214 (H5) in yellow, 255–265 (H6) in purple, 278–282 (EC3) in blue, and 285–286 (H7) in pink. Panels B and C present a close-up view of the binding mode and interactions. Panel C is rotated by 180° around a vertical axis, with respect to panel B. Domains H6 and EC3 are omitted from panel B, and domains H3 and H4 are omitted from panel C, for clarity. H4 and H5 are additionally denoted in panels B and C to assist the reader. In panels B and C, PMX53 atoms are shown in thick licorice; selected C5aR mainchain and side-chain heavy atoms interacting with PMX53 are shown in thin licorice. All atoms are colored by atom type. Hydrogen-bond interactions are shown as black, dashed lines.