Research workbench
Detailed structural insight into the DNA cleavage complex of type iia topoisomerases (cleaved form)
Analyse Detailed structural insight into the DNA cleavage complex of type iia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KSA
- Type
- protein + DNA
- Length
- 1,422 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…
- EC
- 5.99.1.-
- UniProt
- P72525, Q59961
- Ligands
- MG
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 4 subunit a (EC 5.99.1.-) | protein | 474 | 50% helix, 15% strand | P72525 |
| C | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 220 | 40% helix, 16% strand | Q59961 |
| D | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 218 | 40% helix, 17% strand | Q59961 |
| E | 5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*T)-3' | dna | 7 | — | — |
| F | 5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*G P*T)-3' | dna | 11 | — | — |
| G | 5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*T)-3' | dna | 7 | — | — |
| H | 5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*A P*G)-3' | dna | 11 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, E, H, D, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.81 | 0.83 | 84 | empty |
| 2 | 481 | 0.66 | 0.78 | 42 | empty |
| 3 | 355 | 0.66 | 0.80 | 30 | empty |
| 4 | 248 | 0.65 | 0.83 | 25 | empty |
| 5 | 561 | 0.64 | 0.76 | 66 | empty |
Interfaces
22 interfaces between chains.
- B–D · 1716 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1712 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1399 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 808 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 802 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3KSA · Detailed structural insight into the DNA cleavage complex of type IIA topoisomerases… · 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 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 3KSA · PDBe 3KSA · UniProt P72525 · UniProt Q59961
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