MolNFT v1 · #126950 · protein
Structure of the phosphomimetic mutant of the elongation factor ef-tu T62E
5MI9 · Elongation factor tu 1: “Structure of the phosphomimetic mutant of the elongation factor ef-tu T62E”. X-ray diffraction, 2 ligands (GDP, MG), 7 pockets (best druggability 0.76). MolNFT v1 #126950 on GenesisL1: 3D structure, binding…
- PDB
- 5MI9
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu 1
- UniProt
- A8A5E6
- Ligands
- GDP, MG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor tu 1 | protein | 385 | 24% helix, 38% strand | A8A5E6 |
| B | Elongation factor tu 1 | protein | 379 | 23% helix, 36% strand | A8A5E6 |
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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.76 | 0.80 | 115 | empty |
| 2 | 90 | 0.72 | 0.95 | 28 | empty |
| 3 | 51 | 0.64 | 0.94 | 22 | empty |
| 4 | 237 | 0.56 | 0.78 | 39 | empty |
| 5 | 61 | 0.54 | 0.87 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1020 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5MI9 · Structure of the phosphomimetic mutant of the elongation factor EF-Tu T62E · the same entry in another collection · chain B against B, TM-score 1.00
- A8A5E6 · AlphaFold monomer V2.0 prediction for elongation factor tu 1 (A8A5E6) · 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 A8A5E6
- Elsewhere: RCSB PDB 5MI9 · PDBe 5MI9 · UniProt A8A5E6
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