Structure of glycolipid AGSA[20,6P] in complex with mouse CD1D

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 44% strand (DSSP).

Ligands and binding sites

• EMG · N-[(2S,3S,4R)-3,4-dihydroxy-8-oxo-8-[(6-phenylhexyl) amino]-1-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octan-2-yl]icosanamide · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• BMA · beta-D-mannopyranose · sugar
• FUC · alpha-L-fucopyranose · sugar · chains A
• NA · Sodium ion · metal · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1196 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 6C6C · Structure of glycolipid aGSA[20,6P] in complex with mouse CD1d · the same entry in another collection · chain A against A, TM-score 1.00
• P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B 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 A0A0R4J090
• Every structure of UniProt P01887
• Elsewhere: RCSB PDB 6C6C · PDBe 6C6C · UniProt A0A0R4J090 · UniProt P01887