› 1nh3

X-ray diffraction
3.1Å resolution

Human Topoisomerase I Ara-C Complex

Released:
DOI: 10.2210/pdb1nh3/pdb
PDB entry 1nh3 coloured by chain, front view.
PDB entry 1nh3 coloured by chain, side view.
PDB entry 1nh3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural impact of the leukemia drug 1-beta-D-arabinofuranosylcytosine (Ara-C) on the covalent human topoisomerase I-DNA complex.
Chrencik JE, Burgin AB, Pommier Y, Stewart L, Redinbo MR
J Biol Chem 278 12461-6 (2003)
PMID: 12533542

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)
Assembly name:
PDBe Complex ID:
PDB-CPX-113086 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
1 distinct DNA/RNA hybrid molecule
Macromolecules (4 distinct):
DNA topoisomerase 1 Chain: A
Molecule details ›
Chain: A
Length: 563 amino acids
Theoretical weight: 66.73 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P11387 (Residues: 203-765; Coverage: 74%)
Gene name: TOP1
Sequence domains:
Structure domains:
5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*UP*(UBB))-3' Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.02 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*(GNG)P*GP*AP*AP*AP*AP*AP*UP*UP*UP*UP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.56 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*AP*AP*AP*AP*AP*TP*UP*UP*UP*UP*CP*(CAR)P*AP*AP*GP*UP*CP*UP*UP*UP*UP*T)-3' Chain: D
Molecule details ›
Chain: D
Length: 22 nucleotides
Theoretical weight: 6.58 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
2 modified residues:
Ligand CAR 1 x CAR
Ligand PTR 1 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12B
Spacegroup: P32
Unit cell:
a: 72.97Å b: 72.97Å c: 186.29Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.235 0.235 0.311
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

8 review citations

Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases.
Corbett et al. (2004)
7 more

4 mentions without citation

Copaifera of the Neotropics: A Review of the Phytochemistry and Pharmacology.
da Trindade et al. (2018)
3 more