MolNFT v1 · #141647 · protein + DNA
Crystal structure of human topoisomerase II beta in complex with DNA: a new quaternary conformation showing opening of the protein-linked DNA-gate
5ZEN · DNA topoisomerase 2-beta: “Crystal structure of human topoisomerase II beta in complex with DNA: a new quaternary conformation showing…”. X-ray diffraction, 1 ligand (MN), 11 pockets (best druggability 0.75). MolNFT v1 #141647 on…
- PDB
- 5ZEN
- Type
- protein + DNA
- Length
- 725 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-beta; DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3'); DNA…
- EC
- 5.99.1.3
- UniProt
- Q02880
- Ligands
- MN
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-beta (EC 5.99.1.3) | protein | 708 | 48% helix, 15% strand | Q02880 |
| B | DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') | dna | 8 | — | — |
| C | DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3') | dna | 9 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.75 | 0.80 | 85 | MN |
| 2 | 96 | 0.75 | 0.97 | 28 | MN |
| 3 | 444 | 0.73 | 0.83 | 36 | empty |
| 4 | 275 | 0.61 | 0.80 | 33 | empty |
| 5 | 254 | 0.55 | 0.77 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–C · 826 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 819 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 371 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Compared structures
- 5ZEN · Crystal structure of human topoisomerase II beta in complex with DNA: a new quaternary… · the same entry in another collection · chain A against A, TM-score 1.00
- Q02880 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 2-beta (Q02880) · 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 Q02880
- Elsewhere: RCSB PDB 5ZEN · PDBe 5ZEN · UniProt Q02880
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