› 5zad

X-ray diffraction
2.54Å resolution

Human topoisomerase II beta in complex with DNA

Released:
DOI: 10.2210/pdb5zad/pdb
PDB entry 5zad coloured by chain, front view.
PDB entry 5zad coloured by chain, side view.
PDB entry 5zad coloured by chain, top view.
Source organisms:
Primary publication:
Increasing the distance between two monomers of topoisomerase IIβ under the action of antitumor agent 4β-sulfur-(benzimidazole) 4'-demethylepipodophyllotoxin.
Sun LY, Zhu LW, Tang YJ
Sci Rep 8 14949 (2018)
PMID: 30297860

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119488 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA topoisomerase 2-beta Chains: A, B
Molecule details ›
Chains: A, B
Length: 803 amino acids
Theoretical weight: 91.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q02880 (Residues: 450-1206; Coverage: 47%)
Gene name: TOP2B
Sequence domains:
DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 8 nucleotides
Theoretical weight: 2.44 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3') Chains: E, F
Molecule details ›
Chains: E, F
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P32
Unit cell:
a: 95.006Å b: 95.006Å c: 230.289Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.18 0.227
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 citation in other articles

Design, Synthesis and Anti-Tumor Activity of Novel Benzimidazole-Chalcone Hybrids as Non-Intercalative Topoisomerase II Catalytic Inhibitors.
Zhou et al. (2020)
1 more

1 mention without citation

Increasing the distance between two monomers of topoisomerase IIβ under the action of antitumor agent 4β-sulfur-(benzimidazole) 4'-demethylepipodophyllotoxin.
Sun et al. (2018)