MolNFT v1 · #105320 · protein
Re-refined human DNA topoisomerase iia (ATPase and transducer domains) in complex with ADP and SO4
4R1F · DNA topoisomerase 2-alpha: “Re-refined human DNA topoisomerase iia (ATPase and transducer domains) in complex with ADP and SO4”. X-ray diffraction, 3 ligands (ADP, MG, SO4), 13 pockets (best druggability 0.90). MolNFT v1 #105320 on…
- PDB
- 4R1F
- Type
- protein
- Length
- 1,502 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-alpha
- EC
- 5.99.1.3
- UniProt
- P11388
- Ligands
- ADP, MG, SO4
- Pockets
- 13 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-alpha (EC 5.99.1.3) | protein | 366 | 31% helix, 31% strand | P11388 |
| B | DNA topoisomerase 2-alpha (EC 5.99.1.3) | protein | 379 | 35% helix, 30% strand | P11388 |
| C | DNA topoisomerase 2-alpha (EC 5.99.1.3) | protein | 384 | 35% helix, 29% strand | P11388 |
| D | DNA topoisomerase 2-alpha (EC 5.99.1.3) | protein | 373 | 33% helix, 30% 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 · 3 copies · chains B, C, D
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.90 | 0.91 | 152 | MG, ADP, SO4 |
| 2 | 806 | 0.89 | 0.92 | 108 | MG, ADP, GOL, SO4 |
| 3 | 875 | 0.78 | 0.81 | 115 | empty |
| 4 | 85 | 0.57 | 0.87 | 26 | empty |
| 5 | 67 | 0.54 | 0.87 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2433 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2368 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4R1F · Re-refined Human DNA topoisomerase IIa (ATPase and transducer domains) in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P11388 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 2-alpha (P11388) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 4R1F · PDBe 4R1F · UniProt P11388
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