MolNFT v1 · #97783 · protein + DNA
Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate
4KPE · DNA topoisomerase 4 subunit a: “Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate”. X-ray diffraction, 2 ligands (AF5, MG), 14 pockets (best druggability 0.85). MolNFT v1 #97783 on…
- PDB
- 4KPE
- Type
- protein + DNA
- Length
- 1,418 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
- AF5, MG
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 46% 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 | 50% helix, 17% strand | P72525 |
| C | DNA topoisomerase 4 subunit B (EC 5.99.1.3) | protein | 208 | 42% helix, 14% strand | Q59961 |
| D | DNA topoisomerase 4 subunit B (EC 5.99.1.3) | protein | 210 | 43% helix, 15% 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
- AF5 · (7aR,8R)-8-amino-4-cyclopropyl-12-fluoro-1-oxo-4,7,7a,8,9,10-hexahydro-1H-pyrrolo[1',2':1,7]azepino[2,3-h]quinoline-2-carboxylic acid · ligand · 2 copies · chains A, B, C, E, F, H, D, G
- MG · Magnesium ion · metal · 6 copies · chains A, B, G, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.85 | 0.87 | 106 | MG, AF5 |
| 2 | 179 | 0.74 | 0.91 | 26 | MG, AF5 |
| 3 | 623 | 0.67 | 0.77 | 72 | empty |
| 4 | 297 | 0.67 | 0.83 | 25 | empty |
| 5 | 601 | 0.67 | 0.77 | 69 | empty |
Interfaces
22 interfaces between chains.
- A–B · 1524 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1477 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1418 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 690 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 680 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4KPE · Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site… · 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 C 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 4KPE · PDBe 4KPE · UniProt P72525 · UniProt Q59961
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