MolNFT v1 · #97784 · protein + DNA
Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate
4KPF · PARC55: “Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate”. X-ray diffraction, 2 ligands (1UV, MG), 19 pockets (best druggability 0.75). MolNFT v1 #97784 on GenesisL1: 3D structure…
- PDB
- 4KPF
- Type
- protein + DNA
- Length
- 1,418 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PARC55; PARE30; E-SITE1; E-SITE2; E-SITE3; E-SITE4
- UniProt
- P72525, Q59961
- Ligands
- 1UV, MG
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | PARC55 | protein | 482 | 50% helix, 18% strand | P72525 |
| C | PARE30 | protein | 208 | 40% helix, 14% strand | Q59961 |
| D | PARE30 | protein | 210 | 42% helix, 16% strand | Q59961 |
| E | E-SITE1 | dna | 7 | — | — |
| F | E-SITE2 | dna | 11 | — | — |
| G | E-SITE3 | dna | 7 | — | — |
| H | E-SITE4 | dna | 11 | — | — |
Ligands and binding sites
- 1UV · (3aS,4R)-4-amino-13-cyclopropyl-8-fluoro-10-oxo-3a,4,5,6,10,13-hexahydro-1H,3H-pyrrolo[2',1':3,4][1,4]oxazepino[5,6-h]quinoline-11-carboxylic acid · ligand · 2 copies · chains A, B, D, F, G, H, C, E
- MG · Magnesium ion · metal · 6 copies · chains A, E, B, C, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.75 | 0.88 | 42 | MG, 1UV |
| 2 | 267 | 0.74 | 0.88 | 38 | MG, 1UV |
| 3 | 286 | 0.73 | 0.87 | 29 | MG |
| 4 | 317 | 0.66 | 0.81 | 32 | empty |
| 5 | 289 | 0.65 | 0.82 | 30 | empty |
Interfaces
22 interfaces between chains.
- A–B · 1504 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1496 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1406 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 694 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 661 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4KPF · 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 4KPF · PDBe 4KPF · UniProt P72525 · UniProt Q59961
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