Side chain conformational changes between: apo, and holo, and best energy docked solution This figure provides a comparison of the conformations of the apo (4ek3), holo complex (1ykr), and corresponding docked solution with all 12 flexible receptor side-chains displayed as ball-and-sticks. The native bound ligand is displayed as sticks with green carbon atoms and the docked solution is shown with purple carbon atoms and semi-transparent ligand surface. The apo, docked and the holo receptor side-chains are shown with orange, purple and green carbon atoms respectively. The 2 lysine side-chains in the apo conformation overlap with the space occupied by the ligand. All 12 side-chains in the docked solution underwent conformational changes, ranging from small adjustments to large changes needed to resolve steric clashes. The ligand is docked perfectly (RMSD from the crystallographic structure is 0.34 Å) and the receptor side-chains changed their conformations to accommodate the ligand binding in the correct binding mode.
A tutorial is available on this web site in HTML form, or can be downloaded as a PDF file.