Research workbench
E. COLI ef-TU:GDPNP in complex with the antibiotic enacyloxin iia
Analyse E. COLI ef-TU:GDPNP in complex with the antibiotic enacyloxin iia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BVN
- Type
- protein
- Length
- 744 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu
- EC
- 3.6.1.48
- UniProt
- P0A6N1
- Ligands
- GNP, ENX, MG
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor tu (EC 3.6.1.48) | protein | 372 | 24% helix, 38% strand | P0A6N1 |
| B | Elongation factor tu (EC 3.6.1.48) | protein | 372 | 24% helix, 38% strand | P0A6N1 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- ENX · Enacyloxin iia · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.74 | 0.84 | 57 | empty |
| 2 | 673 | 0.72 | 0.79 | 63 | empty |
| 3 | 684 | 0.71 | 0.78 | 64 | empty |
| 4 | 402 | 0.65 | 0.79 | 45 | empty |
| 5 | 394 | 0.64 | 0.78 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 861 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2BVN · E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa · the same entry in another collection · chain A against A, TM-score 1.00
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 P0A6N1
- Elsewhere: RCSB PDB 2BVN · PDBe 2BVN · UniProt P0A6N1
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