Research workbench
QUINOLONE(TROVAFLOXACIN)-DNA cleavage complex of topoisomerase IV from S. pneumoniae
Analyse QUINOLONE(TROVAFLOXACIN)-DNA cleavage complex of topoisomerase IV from S.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z53
- Type
- protein + DNA
- Length
- 1,421 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit a; E-site DNA
- EC
- 5.99.1.3
- UniProt
- Q59961, P72525
- Ligands
- TR6, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit a (EC 5.99.1.3) | protein | 690 | 48% helix, 16% strand | Q59961, P72525 |
| B | DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit a (EC 5.99.1.3) | protein | 695 | 47% helix, 15% strand | Q59961, P72525 |
| E | E-site DNA | dna | 7 | — | — |
| F | E-site DNA | dna | 11 | — | — |
| G | E-site DNA | dna | 7 | — | — |
| H | E-site DNA | dna | 11 | — | — |
Ligands and binding sites
- TR6 · Trovafloxacin · ligand · 2 copies · chains A, B, E, F, H, G
- MG · Magnesium ion · metal · 4 copies · chains A, E, H, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.82 | 0.84 | 81 | MG |
| 2 | 349 | 0.77 | 0.88 | 45 | MG, TR6 |
| 3 | 397 | 0.77 | 0.87 | 52 | MG, TR6 |
| 4 | 315 | 0.69 | 0.83 | 32 | empty |
| 5 | 342 | 0.68 | 0.82 | 32 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2755 Ų buried · 35 hydrogen bonds · protein-protein
- A–F · 878 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–H · 868 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–E · 711 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–G · 703 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 4Z53 · Quinolone(Trovafloxacin)-DNA cleavage complex of topoisomerase IV from S. pneumoniae · 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 0.69
- Q59961 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit B (Q59961) · a predicted model of the same protein · chain A against A, TM-score 0.25
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 Q59961
- Every structure of UniProt P72525
- Elsewhere: RCSB PDB 4Z53 · PDBe 4Z53 · UniProt Q59961 · UniProt P72525
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