Research workbench
Structure of glycolipid AGSA[8,9] in complex with mouse CD1D
Analyse Structure of glycolipid AGSA[8,9] in complex with mouse CD1D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C5M
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin
- UniProt
- A0A0R4J090, P01887
- Ligands
- J81, PLM, NAG, MAN, BMA, FUC
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 267 | 27% helix, 40% strand | A0A0R4J090 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
Ligands and binding sites
- J81 · (5R,6S,7S)-5,6-dihydroxy-N-nonyl-7-(octanoylamino)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl) tetrahydro-2H-pyran-2-yl]oxy}octanamide (non-preferred name) · ligand · chains A
- PLM · Palmitic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.84 | 0.88 | 58 | J81, PLM |
| 2 | 447 | 0.65 | 0.78 | 51 | empty |
| 3 | 201 | 0.47 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1199 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 6C5M · PDBe 6C5M · UniProt A0A0R4J090 · UniProt P01887
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