PDB 1T5W deposited: 2004-05-05 modified: 2009-02-24
Title HLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR)
Authors Anderson, M.W., Gorski, J., Stern, L.J., Strug, I., Zavala-Ruiz, Z.
Structure factors resolution 2.4 rfactor 0.231 rfree 0.255
DPI 0.79 theoretical min: 0.32
Related PDB Entries 1T5X

Peptides bind to class II major histocompatibility complex (MHC) proteins in an extended conformation. Pockets in the peptide binding site spaced to accommodate peptide side chains at the P1, P4, P6, and P9 positions have been previously characterized and help to explain the obtained peptide binding specificity. However, two peptides differing only at P10 have significantly different binding affinities for HLA-DR1. The structure of HLA-DR1 in complex with the tighter binding peptide shows that the peptide binds in the usual polyproline type II conformation, but with the P10 residue accommodated in a shallow pocket at the end of the binding groove. HLA-DR1 variants with polymorphic residues at these positions were produced and found to exhibit different side chain specificity at the P10 position. These results define a new specificity position in HLA-DR proteins.

Chem.Biol. 2004 Oct; 11(10):1395-1402 doi:10.1016/j.chembiol.2004.08.007

Cross References
Database source Identifier Description
PubMed 15489166 CBOLE2
Biomolecule Structure Assembly Serial Assembly Type Conformational State Chains Ligands Atoms
1T5W/1 1T5W 1 trimer 0 3 0 3110
1T5W/2 1T5W 2 trimer 0 3 0 3041