MolNFT v1 · #59463 · protein
A complex between a variant of staphylococcal enterotoxin C3 and the variable domain of the murine T cell receptor beta chain 8.2
3BYT: “A complex between a variant of staphylococcal enterotoxin C3 and the variable domain of the murine T cell…”. X-ray diffraction, 18 pockets (best druggability 0.78). MolNFT v1 #59463 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3BYT
- Type
- protein
- Length
- 1,365 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T cell receptor beta chain 8.2; Enterotoxin type C-3
- UniProt
- P0A0L5
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | T cell receptor beta chain 8.2 | protein | 109 | 3% helix, 51% strand | — |
| B | Enterotoxin type C-3 | protein | 232 | 20% helix, 34% strand | P0A0L5 |
| D | Enterotoxin type C-3 | protein | 233 | 18% helix, 34% strand | P0A0L5 |
| F | Enterotoxin type C-3 | protein | 234 | 17% helix, 32% strand | P0A0L5 |
| H | Enterotoxin type C-3 | protein | 230 | 18% helix, 34% strand | P0A0L5 |
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.78 | 0.80 | 123 | empty |
| 2 | 311 | 0.66 | 0.82 | 39 | empty |
| 3 | 137 | 0.60 | 0.85 | 32 | empty |
| 4 | 249 | 0.59 | 0.79 | 31 | empty |
| 5 | 175 | 0.57 | 0.81 | 34 | empty |
Interfaces
15 interfaces between chains.
- A–B · 620 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 614 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 596 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 542 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 520 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3BYT · A complex between a variant of staphylococcal enterotoxin C3 and the variable domain of… · 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 H against A, TM-score 0.99
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 P0A0L5
- Elsewhere: RCSB PDB 3BYT · PDBe 3BYT · UniProt P0A0L5
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