MolNFT v1 · #148186 · protein
The open conformation of E.COLI elongation factor tu in complex with gdpnp.
6EZE · Elongation factor tu 2: “The open conformation of E.COLI elongation factor tu in complex with gdpnp.”. X-ray diffraction, 3 ligands (GNP, MG, SO4), 8 pockets (best druggability 0.58). MolNFT v1 #148186 on GenesisL1: 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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