Crystal structure of rhesus macaque MHC class I molecule mamu-B*098 complexed with lysophosphatidylethanolamine

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 42% strand (DSSP).

Ligands and binding sites

• EKG · (2R)-2,3-dihydroxypropyl hexadecanoate · ligand · 2 copies · chains A, C
• ZN · Zinc ion · metal · 6 copies · chains A, C, D
• CL · Chloride ion · ion · chains C, D
• EDO · 1,2-ethanediol · additive · 26 copies · chains A, B, C, D
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B, C

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• C–D · 1434 Ų buried · 25 hydrogen bonds · protein-protein
• A–B · 1353 Ų buried · 20 hydrogen bonds · protein-protein
• A–C · 247 Ų buried · 3 hydrogen bonds · protein-protein
• B–C · 44 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 6LAM · Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
• Q6V7J5 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (Q6V7J5) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 A0A1E1GJG5
• Every structure of UniProt Q6V7J5
• Elsewhere: RCSB PDB 6LAM · PDBe 6LAM · UniProt A0A1E1GJG5 · UniProt Q6V7J5