Figure 4

Examples of sub-pockets with low PM ₁₃ Scores. (A) Detail of the superposed binding grooves of [PDB:1BX2] (red) and [PDB:2WBJ] (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 P7 sub-pocket are represented by the larger spheres; these atoms are labelled in blue. The Cα and Cβ atoms of the peptide residues at the P7 positions, remodelled as alanines, are shown with a ball-and-stick representation. (B) Similar to (A), but focusing on the P9 sub-pockets in [PDB:1S9V] (chains A, B, C in red; chains D, E, F in green).