Structure of mouse CD1D with bound alpha-galactosylsphingamide JG168

Structure

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

Ligands and binding sites

• 7LP · (5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide · ligand · chains A
• PLM · Palmitic acid · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
• FUC · alpha-L-fucopyranose · sugar · chains A

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 · 1252 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 5TW2 · Structure of mouse CD1d with bound alpha-galactosylsphingamide JG168 · the same entry in another collection · chain A against A, TM-score 1.00
• P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · chain A against A, TM-score 0.99
• P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P11609
• Every structure of UniProt P01887
• Elsewhere: RCSB PDB 5TW2 · PDBe 5TW2 · UniProt P11609 · UniProt P01887