› 5gwi

X-ray diffraction
2.74Å resolution

Structure of a Human topoisomerase IIbeta fragment in complex with DNA and E7873R

Released:
DOI: 10.2210/pdb5gwi/pdb
PDB entry 5gwi coloured by chain, front view.
PDB entry 5gwi coloured by chain, side view.
PDB entry 5gwi coloured by chain, top view.
Source organisms:
Primary publication:
Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry.
Wang YR, Chen SF, Wu CC, Liao YW, Lin TS, Liu KT, Chen YS, Li TK, Chien TC, Chan NL
Nucleic Acids Res 45 10861-10871 (2017)
PMID: 28977631

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-118718 (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 BL21(DE3)
UniProt:
  • Canonical: Q02880 (Residues: 450-1206; Coverage: 47%)
Gene name: TOP2B
Sequence domains:
Structure domains:
DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') Chains: C, E
Molecule details ›
Chains: C, E
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: D, F
Molecule details ›
Chains: D, F
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand N2R 2 x N2R
Ligand N2N 2 x N2N
Ligand MG 6 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: P21
Unit cell:
a: 79.788Å b: 176.966Å c: 94.528Å
α: 90° β: 112.3° γ: 90°
R-values:
R R work R free
0.215 0.214 0.253
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Topoisomerases as anticancer targets.
Delgado et al. (2018)
2 more

2 mentions without citation

Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry.
Wang et al. (2017)
1 more