Figure 5.

Effect of interfacial layer tilt on docking. (A) and (B) show results at site A for 3NY8 and 3NY9 after aligning the 3NY8 structure to that of 3NY9. The IC interfaces for 3NY8 and 3NY9 are shown as tan and blue spheres, respectively, together with the crystallographically resolved cholesterol for 3NY9 (ball and stick, magenta). In (A), the pose (lines) is shown for 3NY8 (orange) and 3NY9 (green). Residues close to the docked cholesterol (within 4 Å) for 3NY9 are colored blue. Residues close to the docked cholesterol for 3NY8 are colored tan when they are also close to the docked cholesterol for 3NY9 and yellow when only close to the docked cholesterol for 3NY8. (B) shows the effect on poses when the IC interface for 3NY9 is exchanged for that of 3NY8. The crystallographically resolved cholesterol for 3NY9 is shown colored magenta. The pose for 3NY9 with the 3NY9 interface (as in (A)) is colored green and that for 3NY9 with the 3NY8 interface is colored yellow. Residues close to the docked cholesterol for 3NY9 with both the 3NY9 and the 3NY8 interfaces are colored blue. Two residues close to the docked cholesterol only for 3NY9 with the 3NY9 interface are colored tan; the single residue close to the docked cholesterol only for 3NY9 with the 3NY8 interface is colored orange. (C) shows the protein surface at site A for 3NY9 colored by surface depth with cholesterol molecules colored as in (A); the blue bar shows the position of the IC interface for 3NY9. (D) shows the effect of tilt on docking at site d (Fig. 4). The pose for 3NY8 is shown in yellow (ball and stick), but no pose is observed at this site for 3NY9. However, after aligning 3NY9 to 3NY8 and replacing the 3NY9 interface with that of 3NY8, a pose is observed (lines, magenta). Residues close to the docked cholesterol for 3NY8 are shown in tan and those close to the docked cholesterol for 3NY9 with the 3NY8 interface are shown in blue. To see this figure in color, go online.