CD1C in complex with phosphatidylcholine

Structure

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

Ligands and binding sites

• D12 · Dodecane · ligand · chains A
• 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
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
• NA · Sodium ion · metal · chains A
• SO4 · Sulfate ion · ion · chains A, B
• BME · Beta-mercaptoethanol · additive · chains A
• EDO · 1,2-ethanediol · additive · chains A
• MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1364 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 3 glycan, 1 covalent (disulfide, N-glycosylation, additive adduct).

Compared structures

• 6C15 · CD1c in complex with phosphatidylcholine · 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 0.97
• P29017 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1C (P29017) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P29017
• Every structure of UniProt P61769
• Elsewhere: RCSB PDB 6C15 · PDBe 6C15 · UniProt P29017 · UniProt P61769