Research workbench
Crystal structure of the tellurite detoxification protein tehb from E. COLI in complex with sinefungin
Analyse Crystal structure of the tellurite detoxification protein tehb from E. COLI in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XVA
- Type
- protein
- Length
- 782 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tellurite resistance protein tehb
- UniProt
- P25397
- Ligands
- SFG, ZN
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tellurite resistance protein tehb | protein | 199 | 29% helix, 31% strand | P25397 |
| C | Tellurite resistance protein tehb | protein | 190 | 30% helix, 33% strand | P25397 |
| D | Tellurite resistance protein tehb | protein | 194 | 29% helix, 32% strand | P25397 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.56 | 0.74 | 52 | SFG, ZN |
| 2 | 359 | 0.55 | 0.75 | 42 | SFG |
| 3 | 175 | 0.51 | 0.78 | 27 | empty |
| 4 | 221 | 0.47 | 0.74 | 24 | empty |
| 5 | 160 | 0.44 | 0.75 | 22 | SFG |
Interfaces
5 interfaces between chains.
- A–D · 249 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 228 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 194 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 176 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 139 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2XVA · Crystal structure of the tellurite detoxification protein TehB from E. coli in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P25397 · AlphaFold monomer V2.0 prediction for tellurite methyltransferase (P25397) · a predicted model of the same protein · chain C 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 P25397
- Elsewhere: RCSB PDB 2XVA · PDBe 2XVA · UniProt P25397
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