Table 1 Sequence and structural similarity between the eight (DRB1*0402, *0404, *0406, *1401, *1404, *1405, DQB1*0202, and *0503) MHC structural models and their corresponding template structures (1D5Z: DRB1*0401, 1S9V: DQB1*0201, 1UVQ: DQB1*0602). Positives represent a measure of sequence similarity, accounting for identical and conservatively substituted residues. Root mean square deviations (RMSD) values in Å are shown for the Cα atoms of both MHC chains and for the residues comprising the different peptide-binding pockets.

From: Modeling the bound conformation of Pemphigus Vulgaris-associated peptides to MHC Class II DR and DQ Alleles