MolNFT v1 · #123170 · protein
Ef-tu (escherichia COLI) in complex with thiomuracin analog
5JBQ · Elongation factor tu 1: “Ef-tu (escherichia COLI) in complex with thiomuracin analog”. X-ray diffraction, 5 ligands (05N, 6RK, GDP), 1 pocket (best druggability 0.51). MolNFT v1 #123170 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5JBQ
- Type
- protein
- Length
- 403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu 1; Thiomuracin analog
- UniProt
- P0CE47
- Ligands
- 05N, 6RK, GDP, MG, SO4
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor tu 1 | protein | 392 | 25% helix, 38% strand | P0CE47 |
| B | Thiomuracin analog | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- 05N · (3R,4R)-4-hydroxy-3-methyl-L-proline · ligand · chains A, B
- 6RK · 4-azanylcyclohexane-1-carboxylic acid · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.51 | 0.74 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 492 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 3 covalent (nonstandard, covalent ligand).
Compared structures
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 5JBQ · PDBe 5JBQ · UniProt P0CE47
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