Research workbench
Crystal structure of staphylococcal enterotoxin E in complex with a T cell receptor
Analyse Crystal structure of staphylococcal enterotoxin E in complex with a T cell… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UDU
- Type
- protein
- Length
- 640 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T cell receptor alpha chain, T-cell receptor alpha chain C region; Protein TRBV7-9…
- UniProt
- P01848, A0A5A3, A0A5B9, P12993
- Ligands
- NA, ZN
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T cell receptor alpha chain, T-cell receptor alpha chain C region | protein | 184 | 2% helix, 49% strand | P01848 |
| B | Protein TRBV7-9, T-cell receptor beta-2 chain C region | protein | 238 | 8% helix, 50% strand | A0A5A3, A0A5B9 |
| C | Enterotoxin type E | protein | 218 | 21% helix, 35% strand | P12993 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.70 | 0.75 | 74 | empty |
| 2 | 128 | 0.50 | 0.80 | 24 | empty |
| 3 | 57 | 0.49 | 0.86 | 19 | empty |
| 4 | 109 | 0.37 | 0.74 | 24 | empty |
| 5 | 59 | 0.33 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1979 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1023 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4UDU · Crystal structure of staphylococcal enterotoxin E in complex with a T cell receptor · the same entry in another collection · chain A against A, TM-score 1.00
- P12993 · AlphaFold monomer V2.0 prediction for enterotoxin type E (P12993) · a predicted model of the same protein · chain C against A, TM-score 0.99
- A0A5B9 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 2 (A0A5B9) · a predicted model of the same protein · chain B against A, TM-score 0.53
- P01848 · AlphaFold monomer V2.0 prediction for T cell receptor alpha chain constant (P01848) · a predicted model of the same protein · chain A against A, TM-score 0.40
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 P01848
- Every structure of UniProt A0A5A3
- Every structure of UniProt A0A5B9
- Every structure of UniProt P12993
- Elsewhere: RCSB PDB 4UDU · PDBe 4UDU · UniProt P01848 · UniProt A0A5A3 · UniProt A0A5B9 · UniProt P12993
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