Research workbench
QUINOLONE(TROVAFLOXACIN)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae
Analyse QUINOLONE(TROVAFLOXACIN)-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
- 4KOE
- Type
- protein + DNA
- Length
- 1,415 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; E-site DNA1; E-site DNA2…
- EC
- 5.99.1.3
- UniProt
- P72525, Q59961
- Ligands
- TR6, MG
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 4 subunit a (EC 5.99.1.3) | protein | 482 | 49% helix, 18% strand | P72525 |
| C | DNA topoisomerase 4 subunit B (EC 5.99.1.3) | protein | 208 | 45% helix, 14% strand | Q59961 |
| D | DNA topoisomerase 4 subunit B (EC 5.99.1.3) | protein | 207 | 47% helix, 14% strand | Q59961 |
| E | E-site DNA1 | dna | 7 | — | — |
| F | E-site DNA2 | dna | 11 | — | — |
| G | E-site DNA3 | dna | 7 | — | — |
| H | E-site DNA4 | dna | 11 | — | — |
Ligands and binding sites
- TR6 · Trovafloxacin · ligand · 2 copies · chains A, B, C, E, F, H, D, G
- MG · Magnesium ion · metal · 6 copies · chains A, E, H, B, G, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.76 | 0.89 | 47 | MG, TR6 |
| 2 | 280 | 0.74 | 0.87 | 27 | empty |
| 3 | 225 | 0.74 | 0.89 | 40 | MG, TR6 |
| 4 | 330 | 0.68 | 0.83 | 32 | empty |
| 5 | 337 | 0.67 | 0.82 | 32 | empty |
Interfaces
24 interfaces between chains.
- A–B · 1516 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1456 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1424 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 690 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 675 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4KOE · Quinolone(Trovafloxacin)-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 4KOE · PDBe 4KOE · UniProt P72525 · UniProt Q59961
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