Research workbench
Structure of the mouse CD1D-nu-alpha-galcer-inkt TCR complex
Analyse Structure of the mouse CD1D-nu-alpha-galcer-inkt TCR complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QUZ
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2 microglobulin; VALPHA14 (mouse variable…
- UniProt
- P11609, Q91XJ8
- Ligands
- QUV, NAG, FUC
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 266 | 27% helix, 39% strand | P11609 |
| B | Beta-2 microglobulin | protein | 96 | 0% helix, 51% strand | Q91XJ8 |
| C | VALPHA14 (mouse variable domain, human constant domain) | protein | 203 | 5% helix, 47% strand | — |
| D | VBETA8.2 (mouse variable domain, human constant domain) | protein | 239 | 6% helix, 49% strand | — |
Ligands and binding sites
- QUV · N-[(2S,3S,4R)-1-({6-deoxy-6-[(naphthalen-1-ylcarbamoyl)amino]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.85 | 0.85 | 87 | QUV |
| 2 | 972 | 0.70 | 0.75 | 75 | empty |
| 3 | 435 | 0.66 | 0.78 | 46 | empty |
| 4 | 221 | 0.52 | 0.76 | 34 | empty |
| 5 | 147 | 0.44 | 0.76 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2056 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1108 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 479 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 355 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3QUZ · Structure of the mouse CD1d-NU-alpha-GalCer-iNKT TCR complex · 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 1.00
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 Q91XJ8
- Elsewhere: RCSB PDB 3QUZ · PDBe 3QUZ · UniProt P11609 · UniProt Q91XJ8
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