› 3px7

X-ray diffraction
2.3Å resolution

Crystal Structure of covalent complex of topoisomerase 1A with substrate

Released:
DOI: 10.2210/pdb3px7/pdb
PDB entry 3px7 coloured by chain, front view.
PDB entry 3px7 coloured by chain, side view.
PDB entry 3px7 coloured by chain, top view.
Source organism: Escherichia coli DH1
Entry authors: Zhang Z, Tse-dinh YC, Cheng B

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116724 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA topoisomerase 1 Chain: A
Molecule details ›
Chain: A
Length: 595 amino acids
Theoretical weight: 67.28 KDa
Source organism: Escherichia coli DH1
Expression system: Escherichia coli
UniProt:
  • Canonical: P06612 (Residues: 1-595; Coverage: 69%)
Gene names: JW1266, b1274, supX, topA
Sequence domains:
Structure domains:
DNA 5'-D(*TP*TP*GP*GP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 5 nucleotides
Theoretical weight: 1.55 KDa
Source organism: Escherichia coli DH1
Expression system: Not provided
DNA 5'-D(*A*AP*TP*GP*CP*GP*CP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
Source organism: Escherichia coli DH1
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand HG 3 x HG
1 modified residue:
Ligand PTR 1 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 61.602Å b: 91.759Å c: 141.976Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.23 0.269
Expression systems:
  • Escherichia coli
  • Not provided

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