› 2wtf

X-ray diffraction
2.5Å resolution

DNA polymerase eta in complex with the cis-diammineplatinum (II) 1,3- GTG intrastrand cross-link

Released:
DOI: 10.2210/pdb2wtf/pdb
PDB entry 2wtf coloured by chain, front view.
PDB entry 2wtf coloured by chain, side view.
PDB entry 2wtf coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Crystal structure of a cisplatin-(1,3-GTG) cross-link within DNA polymerase eta.
Reissner T, Schneider S, Schorr S, Carell T
Angew Chem Int Ed Engl 49 3077-80 (2010)
PMID: 20333640

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
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-115915 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase eta Chains: A, B
Molecule details ›
Chains: A, B
Length: 536 amino acids
Theoretical weight: 60.71 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q04049 (Residues: 1-513; Coverage: 81%)
Gene names: DBH1, RAD30, YDR419W
Sequence domains: impB/mucB/samB family
Structure domains:
5'-D(*TP*CP*TP*TP*CP*TP*GP*TP*GP*CP *TP*CP*AP*CP*CP*AP*CP)-3' Chains: O, S
Molecule details ›
Chains: O, S
Length: 17 nucleotides
Theoretical weight: 5.09 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
5'-D(*GP*TP*GP*GP*TP*GP*AP*GP*CP)-3' Chains: P, T
Molecule details ›
Chains: P, T
Length: 9 nucleotides
Theoretical weight: 2.81 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DTP 2 x DTP
Ligand CA 10 x CA
Ligand CPT 2 x CPT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P41212
Unit cell:
a: 103.24Å b: 103.24Å c: 292.74Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.227 0.269
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Aromatic rings in chemical and biological recognition: energetics and structures.
Salonen et al. (2011)
9 other articles

2 mentions without citation

Structure-based DNA-targeting strategies with small molecule ligands for drug discovery.
Sheng et al. (2013)
1 more