Research workbench
Human DNA topoisomerase iia ATPASE/ADP
Analyse Human DNA topoisomerase iia ATPASE/ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZXN
- Type
- protein
- Length
- 1,500 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase II, alpha isozyme
- EC
- 5.99.1.3
- UniProt
- P11388
- Ligands
- ADP, MG, SO4
- Pockets
- 12 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase II, alpha isozyme (EC 5.99.1.3) | protein | 366 | 29% helix, 29% strand | P11388 |
| B | DNA topoisomerase II, alpha isozyme (EC 5.99.1.3) | protein | 379 | 35% helix, 28% strand | P11388 |
| C | DNA topoisomerase II, alpha isozyme (EC 5.99.1.3) | protein | 384 | 33% helix, 30% strand | P11388 |
| D | DNA topoisomerase II, alpha isozyme (EC 5.99.1.3) | protein | 371 | 29% helix, 31% strand | P11388 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.90 | 0.92 | 120 | MG, ADP, GOL, SO4 |
| 2 | 1038 | 0.86 | 0.87 | 119 | MG, SO4, ADP |
| 3 | 288 | 0.80 | 0.92 | 33 | MG, ADP |
| 4 | 249 | 0.68 | 0.84 | 38 | empty |
| 5 | 187 | 0.67 | 0.86 | 37 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2263 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2044 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
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 P11388
- Elsewhere: RCSB PDB 1ZXN · PDBe 1ZXN · UniProt P11388
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