Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340 (arginine 327 to citrulline)

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 43% strand (DSSP).

Ligands and binding sites

• CIR · Citrulline · ligand · chains A, B, C
• URE · Urea · ligand · chains B
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, C
• PGE · Triethylene glycol · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 2510 Ų buried · 44 hydrogen bonds · protein-protein
• A–C · 655 Ų buried · 17 hydrogen bonds · protein-protein
• B–C · 624 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

• 5NIG · Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340 (arginine… · the same entry in another collection · chain A against A, TM-score 1.00
• P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
• P06733 · AlphaFold monomer V2.0 prediction for alpha-enolase (P06733) · a predicted model of the same protein · chain C against A, TM-score 0.29

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P01903
• Every structure of UniProt P13760
• Every structure of UniProt P06733
• Elsewhere: RCSB PDB 5NIG · PDBe 5NIG · UniProt P01903 · UniProt P13760 · UniProt P06733