Research workbench
Crystal structure of human topoisomerase II beta in complex with 5- iodouridine-containing-DNA in space group P3221
Analyse Crystal structure of human topoisomerase II beta in complex with 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZQF
- 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/RNA…
- EC
- 5.99.1.3
- UniProt
- Q02880
- Ligands
- MN
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-beta (EC 5.99.1.3) | protein | 708 | 48% helix, 14% strand | Q02880 |
| B | DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') | dna | 8 | — | — |
| C | DNA/RNA (5'-D(P*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)- R(P*(IU))-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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.81 | 0.87 | 69 | MN |
| 2 | 564 | 0.74 | 0.81 | 76 | MN |
| 3 | 219 | 0.55 | 0.79 | 22 | empty |
| 4 | 213 | 0.54 | 0.78 | 38 | empty |
| 5 | 77 | 0.49 | 0.83 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 847 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 813 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 362 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5ZQF · Crystal structure of human topoisomerase II beta in complex with… · 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 5ZQF · PDBe 5ZQF · UniProt Q02880
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