Figure 5

Detail of the binding grooves of HLA-DQ6.2 and HLA-DR4.2. (A) Detail of the binding groove of HLA-DQ6.2 (green). MHC and peptide main chains are represented by a cartoon trace. Spheres indicate the centres of MHC atoms that are determined to be part of the binding groove (see Methods). The centres of MHC atoms that are determined to be part of the P4 sub-pocket are represented by the larger spheres; these atoms are labelled in blue. The Cα and Cβ atoms of the peptide residue at the P7 position, remodelled as alanine, is shown with a ball-and-stick representation. Atoms that differ in binding groove of the model structure of HLA-DQ6.1 are shown in red. (B) Detail of the binding groove of HLA-DR4.2 (red). MHC and peptide main chains are represented by a cartoon trace. Spheres indicate the centres of MHC atoms that are determined to be part of the binding groove (see Methods). Atoms that differ in binding groove of the model structure of HLA-DR4.1 are shown in green. The centres of atoms of residues 70β and 71β are represented by the larger spheres; these atoms are labelled in blue. The Cα and Cβ atoms of the glutamine residue at the P4 position in the peptide are shown with a ball-and-stick representation (yellow).