MolNFT v1 · #69497 · protein + DNA
Detailed structural insight into the DNA cleavage complex of type iia topoisomerases (re-sealed form)
3KSB · DNA topoisomerase 4 subunit a: “Detailed structural insight into the DNA cleavage complex of type iia topoisomerases (re-sealed form)”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.79). MolNFT v1 #69497 on…
- PDB
- 3KSB
- Type
- protein + DNA
- Length
- 1,409 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 4 subunit a; DNA topoisomerase 4 subunit B…
- EC
- 5.99.1.-
- UniProt
- P72525, Q59961
- Ligands
- MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 4 subunit a (EC 5.99.1.-) | protein | 471 | 51% helix, 14% strand | P72525 |
| C | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 217 | 38% helix, 17% strand | Q59961 |
| D | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 214 | 38% helix, 17% strand | Q59961 |
| E | 5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*TP*GP*AP*CP* TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3' | dna | 18 | — | — |
| F | 5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*TP*AP*GP*TP* CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3' | dna | 18 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, C, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.79 | 0.83 | 72 | empty |
| 2 | 92 | 0.76 | 0.97 | 30 | empty |
| 3 | 475 | 0.67 | 0.79 | 46 | empty |
| 4 | 343 | 0.65 | 0.80 | 34 | empty |
| 5 | 443 | 0.65 | 0.78 | 47 | empty |
Interfaces
14 interfaces between chains.
- B–D · 1670 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1664 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1356 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 852 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- B–C · 802 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3KSB · Detailed structural insight into the DNA cleavage complex of type IIA topoisomerases… · the same entry in another collection · chain F against F, 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 D against A, TM-score 0.93
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 3KSB · PDBe 3KSB · UniProt P72525 · UniProt Q59961
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