Figure 2 - full size

 

Figure 2.
Figure 2. Structure of the HLA-DR1-A2 peptide binding site. (a) Top view of the peptide-binding site, with HLA-DR1 residues in contact with the peptide indicated with sidechain or mainchain atoms as appropriate. Atoms are colored by atom type, with oxygen in red, nitrogen in blue and carbon atoms in green for the peptide and yellow for HLA-DR1. The peptide residues are numbered, with Trp(+1) in the principal binding pocket; hydrogen bonds are shown in magenta. (b) Schematic diagram of peptide hydrogen-bonding interactions. The peptide sidechains are shown as R[n] except for arginine at position 2 which contacts the HLA-DR1 mainchain carbonyl b77 at a kink in the b-chain helical region. The sidechain of His(+8) is also positioned to form a hydrogen bond with HLA-DR1 (not shown). The peptide mainchain is shaded in green. The interactions are color-coded: HLA-DR1-peptide hydrogen bonds, yellow; hydrogen bonds to buried water molecules, pink; hydrogen bonds to exposed water molecules, blue; Arg(+2) guanidinium-HLA-DR1 b77 carbonyl hydrogen bond, red. (c) Top view of the peptide-binding site, with the molecular surface indicated by blue dots. A Ca trace for HLA-DR1 is shown together with a stick model for the A2 peptide and buried water molecules; bonds are colored by atom type and water molecules are shown as spheres. Not all water molecules are observed in each molecule in the asymmetric unit.

The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 1385-1396) copyright 1997.