Research workbench
Crystal structure of mouse CD1D in complex with ganglioside GD3
Analyse Crystal structure of mouse CD1D in complex with ganglioside GD3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AU1
- 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
- P11609, P01887
- Ligands
- ERA, NAG, MAN, GLC, BMA, FUC, BGC, GAL
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 267 | 26% helix, 42% strand | P11609 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
Ligands and binding sites
- ERA · (7Z,15E,17E)-N-[(2S,3S,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tricosa-7,15,17-trienamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- GLC · alpha-D-glucopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar
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 | 674 | 0.85 | 0.88 | 59 | ERA |
| 2 | 389 | 0.63 | 0.78 | 43 | empty |
| 3 | 223 | 0.49 | 0.74 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1182 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3AU1 · Crystal structure of mouse CD1d in complex with ganglioside GD3 · 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 0.98
- 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 P11609
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 3AU1 · PDBe 3AU1 · UniProt P11609 · UniProt P01887
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