MolNFT v1 · #18639 · protein
Crystal structure of the ATPase region of saccharomyces cerevisiae topoisomerase II
1PVG · DNA topoisomerase II: “Crystal structure of the ATPase region of saccharomyces cerevisiae topoisomerase II”. X-ray diffraction, 2 ligands (ANP, MG), 10 pockets (best druggability 0.81). MolNFT v1 #18639 on GenesisL1: 3D structure…
- PDB
- 1PVG
- Type
- protein
- Length
- 756 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase II
- EC
- 5.99.1.3
- UniProt
- P06786
- Ligands
- ANP, MG
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase II (EC 5.99.1.3) | protein | 378 | 32% helix, 28% strand | P06786 |
| B | DNA topoisomerase II (EC 5.99.1.3) | protein | 378 | 33% helix, 28% strand | P06786 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.81 | 0.92 | 39 | MG, ANP |
| 2 | 1071 | 0.79 | 0.81 | 101 | empty |
| 3 | 297 | 0.78 | 0.90 | 40 | MG, ANP |
| 4 | 61 | 0.71 | 0.98 | 17 | empty |
| 5 | 186 | 0.56 | 0.80 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2675 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1PVG · Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II · the same entry in another collection · chain A against A, TM-score 1.00
- P06786 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 2 (P06786) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P06786
- Elsewhere: RCSB PDB 1PVG · PDBe 1PVG · UniProt P06786
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