MolNFT v1 · #85875 · protein
Crystal structure of autoreactive-VALPHA14-VBETA6 nkt TCR in complex with CD1D-sulfatide
4APQ · Antigen-presenting glycoprotein CD1D1: “Crystal structure of autoreactive-VALPHA14-VBETA6 nkt TCR in complex with CD1D-sulfatide”. X-ray diffraction, 4 ligands (CIS, NAG, BMA), 8 pockets (best druggability 0.86). MolNFT v1 #85875 on…
- PDB
- 4APQ
- Type
- protein
- Length
- 825 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Mouse nkt TCR VALPHA14…
- UniProt
- P11609, P01887
- Ligands
- CIS, NAG, BMA, MAN
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 290 | 26% helix, 39% strand | P11609 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 47% strand | P01887 |
| C | Mouse nkt TCR VALPHA14, human nkt TCR VALPHA14 | protein | 196 | 3% helix, 47% strand | — |
| D | Mouse nkt TCR autoreactive-VBETA6, human nkt TCR autoreactive-VBETA6 | protein | 240 | 5% helix, 51% strand | — |
Ligands and binding sites
- CIS · (15Z)-N-((1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-enyl)tetracos-15-enamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.86 | 0.88 | 76 | CIS |
| 2 | 1013 | 0.70 | 0.75 | 81 | empty |
| 3 | 391 | 0.64 | 0.79 | 56 | empty |
| 4 | 160 | 0.53 | 0.80 | 32 | empty |
| 5 | 188 | 0.49 | 0.76 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2044 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1646 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 470 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 337 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4APQ · Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-sulfatide · the same entry in another collection · chain A against A, TM-score 1.00
- 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
- 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 0.96
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 P11609
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 4APQ · PDBe 4APQ · UniProt P11609 · UniProt P01887
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