MolNFT v1 · #68888 · protein + DNA
Detailed structural insight into the quinolone-DNA cleavage complex of type iia topoisomerases
3K9F · DNA topoisomerase 4 subunit a: “Detailed structural insight into the quinolone-DNA cleavage complex of type iia topoisomerases”. X-ray diffraction, 2 ligands (LFX, MG), 17 pockets (best druggability 0.83). MolNFT v1 #68888 on…
- PDB
- 3K9F
- Type
- protein + DNA
- Length
- 1,442 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; DNA…
- EC
- 5.99.1.-
- UniProt
- P72525, Q59961
- Ligands
- LFX, MG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 4 subunit a (EC 5.99.1.-) | protein | 481 | 50% helix, 17% strand | P72525 |
| C, D | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 222 | 41% helix, 18% strand | Q59961 |
| E | DNA (5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*T)-3') | dna | 7 | — | — |
| F | DNA (5'- D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3') | dna | 11 | — | — |
| G | DNA (5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*T)-3') | dna | 7 | — | — |
| H | DNA (5'- D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3') | dna | 11 | — | — |
Ligands and binding sites
- LFX · (3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid · ligand · 2 copies · chains A, B, C, E, F, H, D, G
- MG · Magnesium ion · metal · 2 copies · chains C, E, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.83 | 0.85 | 74 | empty |
| 2 | 120 | 0.74 | 0.95 | 21 | MG |
| 3 | 121 | 0.74 | 0.94 | 21 | MG |
| 4 | 1090 | 0.73 | 0.76 | 109 | empty |
| 5 | 681 | 0.70 | 0.77 | 74 | empty |
Interfaces
22 interfaces between chains.
- A–C · 1665 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1660 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1472 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 934 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 932 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3K9F · Detailed structural insight into the quinolone-DNA cleavage complex of type IIA… · 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 A against A, TM-score 0.97
- 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 0.96
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 3K9F · PDBe 3K9F · UniProt P72525 · UniProt Q59961
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