Research workbench
Crystal structure of human topoisomerase II beta in complex with 5- iodouridine-containing-DNA and etoposide in space group P21
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
- 5ZRF
- Type
- protein + DNA
- Length
- 1,380 residues
- Chains
- 6
- 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
- EVP, MG
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-beta (EC 5.99.1.3) | protein | 669 | 50% helix, 14% strand | Q02880 |
| B | DNA topoisomerase 2-beta (EC 5.99.1.3) | protein | 671 | 49% helix, 14% strand | Q02880 |
| C, E | DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') | dna | 8 | — | — |
| D, F | DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))- D(P*CP*GP*GP*C)-R(P*(IU))-3') | dna | 12 | — | — |
Ligands and binding sites
- EVP · (5s,5ar,8ar,9r)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5A,6,8,8A,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside · ligand · 2 copies · chains B, D, E, F, A, C
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, E, D, F
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 | 1065 | 0.83 | 0.84 | 96 | EVP |
| 2 | 658 | 0.81 | 0.86 | 61 | MG |
| 3 | 534 | 0.76 | 0.83 | 53 | MG |
| 4 | 397 | 0.61 | 0.77 | 46 | empty |
| 5 | 345 | 0.59 | 0.77 | 40 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1485 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 959 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–F · 936 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–E · 814 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 735 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 5ZRF · Crystal structure of human topoisomerase II beta in complex with… · the same entry in another collection · chain F against F, 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 5ZRF · PDBe 5ZRF · UniProt Q02880
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