MolNFT v1 · #82754 · protein
Ternary crystal structure of the human nkt TCR-CD1D-4'DEOXY-alpha- galactosylceramide complex
3VWK · Antigen-presenting glycoprotein CD1D: “Ternary crystal structure of the human nkt TCR-CD1D-4'DEOXY-alpha- galactosylceramide complex”. X-ray diffraction, 3 ligands (4GH, NAG, MG), 9 pockets (best druggability 0.87). MolNFT v1 #82754…
- PDB
- 3VWK
- Type
- protein
- Length
- 781 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D; Beta-2-microglobulin; NKT15 T cell receptor…
- UniProt
- P15813, P61769
- Ligands
- 4GH, NAG, MG
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D | protein | 249 | 26% helix, 38% strand | P15813 |
| B | Beta-2-microglobulin | protein | 96 | 0% helix, 53% strand | P61769 |
| C | NKT15 T cell receptor alpha-chain | protein | 194 | 5% helix, 49% strand | — |
| D | NKT15 T cell receptor beta-chain | protein | 242 | 7% helix, 49% strand | — |
Ligands and binding sites
- 4GH · N-{(2S,3R)-1-[(4-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}hexacosanamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.87 | 0.89 | 75 | 4GH |
| 2 | 636 | 0.65 | 0.75 | 75 | empty |
| 3 | 341 | 0.62 | 0.78 | 41 | empty |
| 4 | 188 | 0.53 | 0.78 | 24 | empty |
| 5 | 227 | 0.51 | 0.76 | 30 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2013 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1096 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 467 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 330 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3VWK · Ternary crystal structure of the human NKT TCR-CD1d-4'deoxy-alpha-galactosylceramide… · the same entry in another collection · chain A against A, TM-score 1.00
- P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P15813
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3VWK · PDBe 3VWK · UniProt P15813 · UniProt P61769
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