› 1k4t

X-ray diffraction
2.1Å resolution

HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX

Released:
DOI: 10.2210/pdb1k4t/pdb
PDB 1k4t coloured by chain and viewed from the front.
PDB 1k4t coloured by chain and viewed from the side.
PDB 1k4t coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
The mechanism of topoisomerase I poisoning by a camptothecin analog.
Staker BL, Hjerrild K, Feese MD, Behnke CA, Burgin AB, Stewart L
Proc. Natl. Acad. Sci. U.S.A. 99 15387-92 (2002)
PMID: 12426403

Function and Biology Details

Reaction catalysed: 
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA topoisomerase 1 Chain: A
Molecule details ›
Chain: A
Length: 592 amino acids
Theoretical weight: 70.25 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P11387 (Residues: 174-765; Coverage: 77%)
Gene name: TOP1
Sequence domains:
Structure domains:
5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3' Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.72 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3' Chain: D
Molecule details ›
Chain: D
Length: 22 nucleotides
Theoretical weight: 6.69 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand TTG 1 x TTG
Ligand TTC 1 x TTC
Ligand HG 1 x HG
Ligand PG4 1 x PG4
2 modified residues:
Ligand TGP 1 x TGP
Ligand PTR 1 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 57.093Å b: 116.26Å c: 75.217Å
α: 90° β: 94.16° γ: 90°
R-values:
R R work R free
0.229 0.229 0.269
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

56 review citations

Excision repair of topoisomerase DNA-protein crosslinks (TOP-DPC).
Sun et al. (2020)
55 more

42 mentions without citation

Recent developments in topoisomerase-targeted cancer chemotherapy.
Hevener et al. (2018)
41 more