Figure 2 - full size

 

Figure 2.
Fig. 2. A shows schematically the interactions of HCA II with the R (Left) and S (Right) stereoisomers grown by CombiSMoG. The surface of the protein is represented by a black curve, on which the approximate positions of the protein residues contacting the ligand are indicated. Three distinct binding pockets are separated by Pro-202 and Phe-131. The red arrows indicate the contacts between the ligand and the protein residues. The predicted and x-ray binding conformations of the R (Left) and S (Right) ligands are compared in B. The conformations predicted by CombiSMoG are colored red, and the x-ray difference electron density maps are shown in purple. These maps were calculated with Fourier coefficients |Fo| |Fc| and phases derived from the final model less the inhibitor and active-site solvent molecules; their contours are at 2 sigma. The fits to the electron density maps are shown in yellow. There are two different viewing angles: the top shows the contacts formed by methyl groups, and the bottom illustrates the interactions of the indole group with the protein. The protein residues making contacts with these groups are marked by letter codes.