MolNFT v1 · #126944 · protein
Structure of phosphorylated translation elongation factor ef-tu from E. COLI
5MI3 · Elongation factor tu 1: “Structure of phosphorylated translation elongation factor ef-tu from E. COLI”. X-ray diffraction, 2 ligands (GDP, MG), 6 pockets (best druggability 0.59). MolNFT v1 #126944 on GenesisL1: 3D structure…
- PDB
- 5MI3
- Type
- protein
- Length
- 772 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu 1
- UniProt
- P0CE47
- Ligands
- GDP, MG
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Elongation factor tu 1 | protein | 386 | 25% helix, 39% strand | P0CE47 |
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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.59 | 0.80 | 34 | empty |
| 2 | 383 | 0.56 | 0.74 | 47 | empty |
| 3 | 307 | 0.55 | 0.76 | 56 | empty |
| 4 | 54 | 0.33 | 0.78 | 14 | empty |
| 5 | 57 | 0.29 | 0.75 | 20 | MG, GDP |
Interfaces
1 interface between chains.
- A–B · 1281 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5MI3 · Structure of phosphorylated translation elongation factor EF-Tu from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
- P0CE47 · AlphaFold monomer V2.0 prediction for elongation factor tu 1 (P0CE47) · 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 P0CE47
- Elsewhere: RCSB PDB 5MI3 · PDBe 5MI3 · UniProt P0CE47
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