Research workbench
Structure of the mouse invariant nkt cell receptor VALPHA14
Analyse Structure of the mouse invariant nkt cell receptor VALPHA14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q86
- Type
- protein
- Length
- 845 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VALPHA14 TCR; VBETA8.2
- Ligands
- NAG, BMA, FUC, MAN
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VALPHA14 TCR | protein | 189 | 5% helix, 49% strand | — |
| B, D | VBETA8.2 | protein | 233 | 7% helix, 55% strand | — |
| C | VALPHA14 TCR | protein | 190 | 4% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.72 | 0.83 | 62 | empty |
| 2 | 157 | 0.59 | 0.83 | 36 | empty |
| 3 | 239 | 0.59 | 0.79 | 36 | empty |
| 4 | 69 | 0.59 | 0.90 | 21 | empty |
| 5 | 185 | 0.59 | 0.81 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1969 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1894 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1010 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 326 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 243 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2Q86 · Structure of the mouse invariant NKT cell receptor Valpha14 · the same entry in another collection · 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
- Elsewhere: RCSB PDB 2Q86 · PDBe 2Q86
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