Research workbench
The open conformation of E.COLI elongation factor tu in complex with gdpnp.
Analyse The open conformation of E.COLI elongation factor tu in complex with gdpnp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EZE
- Type
- protein
- Length
- 772 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu 2
- UniProt
- P0CE48
- Ligands
- GNP, MG, SO4
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Elongation factor tu 2 | protein | 386 | 24% helix, 38% strand | P0CE48 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.58 | 0.74 | 51 | PEG |
| 2 | 292 | 0.57 | 0.77 | 36 | empty |
| 3 | 294 | 0.52 | 0.74 | 50 | GOL |
| 4 | 191 | 0.50 | 0.77 | 39 | empty |
| 5 | 113 | 0.36 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1115 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6EZE · The open conformation of E.coli Elongation Factor Tu in complex with GDPNP. · the same entry in another collection · chain A against A, TM-score 1.00
- P0CE48 · AlphaFold monomer V2.0 prediction for elongation factor tu 2 (P0CE48) · a predicted model of the same protein · chain A 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 P0CE48
- Elsewhere: RCSB PDB 6EZE · PDBe 6EZE · UniProt P0CE48
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