Research workbench
Crystal structure of T-cell receptor V beta domain variant complexed with superantigen SEC3 mutant
Analyse Crystal structure of T-cell receptor V beta domain variant complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AQ1
- Type
- protein
- Length
- 1,380 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell receptor beta chain V; Enterotoxin type C-3
- UniProt
- P04213, P0A0L5
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | T-cell receptor beta chain V | protein | 109 | 3% helix, 52% strand | P04213 |
| B | Enterotoxin type C-3 | protein | 234 | 19% helix, 35% strand | P0A0L5 |
| D | Enterotoxin type C-3 | protein | 236 | 19% helix, 33% strand | P0A0L5 |
| F, H | Enterotoxin type C-3 | protein | 237 | 19% helix, 33% strand | P0A0L5 |
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.81 | 0.83 | 108 | empty |
| 2 | 392 | 0.60 | 0.76 | 44 | empty |
| 3 | 241 | 0.59 | 0.79 | 32 | empty |
| 4 | 379 | 0.58 | 0.75 | 36 | empty |
| 5 | 200 | 0.56 | 0.80 | 29 | empty |
Interfaces
11 interfaces between chains.
- E–F · 645 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 591 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 573 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 563 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 434 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2AQ1 · Crystal structure of T-cell receptor V beta domain variant complexed with superantigen… · the same entry in another collection · chain H against H, TM-score 1.00
- P0A0L5 · AlphaFold monomer V2.0 prediction for enterotoxin type C-3 (P0A0L5) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P04213 · AlphaFold monomer V2.0 prediction for T-cell receptor beta chain V region C5 (P04213) · a predicted model of the same protein · chain A 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 P04213
- Every structure of UniProt P0A0L5
- Elsewhere: RCSB PDB 2AQ1 · PDBe 2AQ1 · UniProt P04213 · UniProt P0A0L5
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