Research workbench
QUINOLONE(CLINAFLOXACIN)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae
Analyse QUINOLONE(CLINAFLOXACIN)-DNA cleavage complex of type IV topoisomerase from S.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RAD
- Type
- protein + DNA
- Length
- 1,417 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 4 subunit a; DNA topoisomerase 4 subunit B…
- EC
- 5.99.1.-
- UniProt
- P72525, Q59961
- Ligands
- NFX, MG
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 4 subunit a (EC 5.99.1.-) | protein | 482 | 50% helix, 17% strand | P72525 |
| C | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 209 | 37% helix, 13% strand | Q59961 |
| D | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 208 | 43% helix, 14% strand | Q59961 |
| E | 5'-D(*CP*AP*TP*GP*AP*AP*T)-3' | dna | 7 | — | — |
| F | 5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3' | dna | 11 | — | — |
| G | 5'-D(*CP*GP*TP*GP*CP*AP*T)-3' | dna | 7 | — | — |
| H | 5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*G)-3' | dna | 11 | — | — |
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 A, B, C, E, F, H, D, G
- MG · Magnesium ion · metal · 6 copies · chains A, E, F, B, G, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.83 | 0.84 | 99 | MG, NFX |
| 2 | 745 | 0.74 | 0.79 | 82 | MG |
| 3 | 444 | 0.67 | 0.79 | 54 | MG |
| 4 | 299 | 0.66 | 0.82 | 29 | empty |
| 5 | 278 | 0.64 | 0.82 | 28 | empty |
Interfaces
22 interfaces between chains.
- A–B · 1490 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1442 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1399 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 708 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 677 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3RAD · Quinolone(Clinafloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae · the same entry in another collection · chain H against H, TM-score 1.00
- 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 0.98
- P72525 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit a (P72525) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 3RAD · PDBe 3RAD · UniProt P72525 · UniProt Q59961
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