Research workbench
Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases
Analyse Structural insight into the quinolone-DNA cleavage complex of type IIA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FOE
- Type
- protein + DNA
- Length
- 1,327 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.001
- Source
- Streptococcus pneumoniae; SYNTHETIC CONSTRUCT
- Molecule
- DNA topoisomerase 4 subunit A; DNA topoisomerase 4 subunit B; DNA…
- EC
- 5.99.1.-
- UniProt
- P72525, Q59961
- Ligands
- NFX
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · resolution 4.001 · 8 distinct chains · 44% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 4 subunit A (EC 5.99.1.-) | protein | 432 | 50% helix, 7% strand | P72525 |
| B | DNA topoisomerase 4 subunit A (EC 5.99.1.-) | protein | 433 | 50% helix, 7% strand | P72525 |
| C | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 196 | 30% helix, 6% strand | Q59961 |
| D | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 198 | 29% helix, 7% strand | Q59961 |
| E | DNA (5'-D(P*AP*CP*CP*AP*AP*GP*GP*TP*CP*AP*TP*GP*AP*AP*T)-3') | dna | 15 | — | — |
| F | DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3') | dna | 19 | — | — |
| G | DNA (5'-D(P*CP*TP*GP*TP*TP*TP*TP*AP*CP*GP*TP*GP*CP*AP*T)-3') | dna | 15 | — | — |
| H | DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3') | dna | 19 | — | — |
Ligands and binding sites
- NFX · 7-[(3R)-3-aminopyrrolidin-1-yl]-8-chloro-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid · ligand · 2 copies · chains B, F, G, H, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.87 | 0.89 | 140 | empty |
| 2 | 1171 | 0.85 | 0.86 | 161 | empty |
| 3 | 749 | 0.84 | 0.88 | 108 | empty |
| 4 | 658 | 0.83 | 0.88 | 101 | empty |
| 5 | 821 | 0.76 | 0.80 | 88 | empty |
Interfaces
22 interfaces between chains.
- A–B · 896 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 706 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 702 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 676 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- E–F · 675 Ų buried · 56 hydrogen bonds · nucleic-nucleic
Compared structures
- 3FOE · Structural insight into the quinolone-DNA cleavage complex of type iia topoisomerases · the same entry in another collection · chain H against H, TM-score 1.00
- P72525 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit a (P72525) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q59961 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit B (Q59961) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 P72525
- Every structure of UniProt Q59961
- Elsewhere: RCSB PDB 3FOE · PDBe 3FOE · UniProt P72525 · UniProt Q59961
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