Human CD1B in complex with endogenous phosphatidylcholine and spacer

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 44% strand (DSSP).

Ligands and binding sites

• 6PL · (4S,7R)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · chains A
• 6UL · Tetracosyl palmitate · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
• SO4 · Sulfate ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1383 Ų buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 2H26 · human CD1b in complex with endogenous phosphatidylcholine and spacer · the same entry in another collection · chain A against A, TM-score 1.00
• 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
• 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 0.97

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 2H26 · PDBe 2H26 · UniProt P29016 · UniProt P61769