Crystal structure of the mouse CD1D in complex with the P99 peptide

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 42% strand (DSSP).

Ligands and binding sites

• 6UL · Tetracosyl palmitate · ligand · chains A, C
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
• BMA · beta-D-mannopyranose · sugar
• MAN · alpha-D-mannopyranose · sugar · chains A
• FUC · alpha-L-fucopyranose · sugar · chains A
• GOL · Glycerol · additive · 4 copies · chains A, B
• TAR · D(-)-tartaric acid · additive · chains 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

2 interfaces between chains.

• A–B · 1246 Ų buried · 14 hydrogen bonds · protein-protein
• A–C · 968 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 5FKP · Crystal structure of the mouse CD1d in complex with the p99 peptide · 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 5FKP · PDBe 5FKP · UniProt P11609 · UniProt P01887