› 6mxo

X-ray diffraction
2.04Å resolution

Structure of HPoleta incorporating dCTP opposite the 3-prime Pt(DACH)-GG

Released:
DOI: 10.2210/pdb6mxo/pdb
PDB entry 6mxo coloured by chain, front view.
PDB entry 6mxo coloured by chain, side view.
PDB entry 6mxo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for the bypass of the major oxaliplatin-DNA adducts by human DNA polymerase η.
Ouzon-Shubeita H, Baker M, Koag MC, Lee S
Biochem J 476 747-758 (2019)
PMID: 30709915

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-120308 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase eta Chain: A
Molecule details ›
Chain: A
Length: 442 amino acids
Theoretical weight: 49.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y253 (Residues: 3-435; Coverage: 61%)
Gene names: POLH, RAD30, RAD30A, XPV
Sequence domains:
Structure domains:
DNA (5'-D(*AP*CP*GP*GP*CP*TP*CP*AP*CP*AP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.61 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*TP*AP*GP*TP*GP*TP*GP*AP*G)-3') Chain: P
Molecule details ›
Chain: P
Length: 9 nucleotides
Theoretical weight: 2.81 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand 0KX 1 x 0KX
Ligand MG 2 x MG
Ligand GOL 3 x GOL
Ligand 9RD 1 x 9RD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P61
Unit cell:
a: 98.56Å b: 98.56Å c: 81.713Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.177 0.175 0.23
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

For the Better or for the Worse? The Effect of Manganese on the Activity of Eukaryotic DNA Polymerases.
Balint et al. (2023)
1 more

2 mentions without citation

Structural basis for the bypass of the major oxaliplatin-DNA adducts by human DNA polymerase η.
Ouzon-Shubeita et al. (2019)
1 more