MolNFT v1 · #190969 · protein
Human topoisomerase II beta ATPase ADP
7ZBG · DNA topoisomerase 2-beta: “Human topoisomerase II beta ATPase ADP”. X-ray diffraction, 4 ligands (ADP, ITH, MG), 4 pockets (best druggability 0.77). MolNFT v1 #190969 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ZBG
- Type
- protein
- Length
- 363 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-beta
- EC
- 5.6.2.2
- UniProt
- Q02880
- Ligands
- ADP, ITH, MG, SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-beta (EC 5.6.2.2) | protein | 363 | 30% helix, 29% strand | Q02880 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ITH · 4-[(2S,3R)-3-[3,5-bis(oxidanylidene)piperazin-1-ium-1-yl]butan-2-yl]piperazin-4-ium-2,6-dione · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.77 | 0.86 | 58 | ADP, SO4, MG |
| 2 | 175 | 0.58 | 0.81 | 30 | empty |
| 3 | 76 | 0.54 | 0.86 | 20 | empty |
| 4 | 65 | 0.34 | 0.77 | 16 | empty |
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 Q02880
- Elsewhere: RCSB PDB 7ZBG · PDBe 7ZBG · UniProt Q02880
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