Research workbench
Structure of TSE6 in complex with ef-tu
Analyse Structure of TSE6 in complex with ef-tu in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZV4
- Type
- protein
- Length
- 1,105 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu; TSE6
- UniProt
- P09591, Q9I739
- Ligands
- GDP, MG
- Pockets
- 13 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor tu | protein | 392 | 20% helix, 36% strand | P09591 |
| C | TSE6 | protein | 162 | 27% helix, 28% strand | Q9I739 |
| D | TSE6 | protein | 163 | 28% helix, 28% strand | Q9I739 |
| B | Elongation factor tu | protein | 388 | 20% helix, 36% strand | P09591 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.62 | 0.81 | 31 | empty |
| 2 | 205 | 0.61 | 0.82 | 24 | empty |
| 3 | 248 | 0.60 | 0.79 | 30 | empty |
| 4 | 307 | 0.51 | 0.73 | 40 | empty |
| 5 | 84 | 0.50 | 0.84 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–C · 782 Ų buried · 13 hydrogen bonds · protein-protein
- D–B · 729 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 199 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 185 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 110 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZV4 · Structure of Tse6 in complex with EF-Tu · the same entry in another collection · chain B against B, TM-score 1.00
- Q9I739 · AlphaFold monomer V2.0 prediction for NAD(P)(+) glycohydrolase toxin TSE6 (Q9I739) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P09591 · AlphaFold monomer V2.0 prediction for elongation factor tu (P09591) · a predicted model of the same protein · chain B against A, TM-score 0.59
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 P09591
- Every structure of UniProt Q9I739
- Elsewhere: RCSB PDB 4ZV4 · PDBe 4ZV4 · UniProt P09591 · UniProt Q9I739
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