MolNFT v1 · #64157 · protein
Crystal structure of E. COLI topoisomerase IV co-complexed with inhibitor
3FV5 · DNA topoisomerase 4 subunit B: “Crystal structure of E. COLI topoisomerase IV co-complexed with inhibitor”. X-ray diffraction, 1 ligand (1EU), 3 pockets (best druggability 0.48). MolNFT v1 #64157 on GenesisL1: 3D structure, binding…
- PDB
- 3FV5
- Type
- protein
- Length
- 361 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 4 subunit B
- EC
- 5.99.1.-
- UniProt
- P20083
- Ligands
- 1EU
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 180 | 29% helix, 34% strand | P20083 |
| B | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 181 | 30% helix, 35% strand | P20083 |
Ligands and binding sites
- 1EU · 1-(4-acetyl-6-pyridin-3-yl-1H-benzimidazol-2-yl)-3-ethylurea · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.48 | 0.81 | 18 | 1EU |
| 2 | 74 | 0.40 | 0.79 | 16 | 1EU |
| 3 | 126 | 0.37 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 232 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3FV5 · Crystal Structure of E. coli Topoisomerase IV co-complexed with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P20083 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit B (P20083) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P20083
- Elsewhere: RCSB PDB 3FV5 · PDBe 3FV5 · UniProt P20083
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