Crystal structure of human CD1B in complex with ps

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 45% strand (DSSP).

Ligands and binding sites

• CUY · tetracosyl octadecanoate · ligand · chains A
• P50 · (19S,22S,25R)-25-amino-22-hydroxy-16,22,26-trioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
• FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• BMA · beta-D-mannopyranose · sugar
• NA · Sodium ion · metal · 3 copies · chains B, A
• CL · Chloride ion · ion · 7 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1260 Ų buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

• 5WKE · Crystal Structure of Human CD1b in Complex with PS · the same entry in another collection · chain B against B, TM-score 1.00
• P29016 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1B (P29016) · a predicted model of the same protein · chain A against A, TM-score 0.98
• P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B 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 P29016
• Every structure of UniProt P61769
• Elsewhere: RCSB PDB 5WKE · PDBe 5WKE · UniProt P29016 · UniProt P61769