› 3pzp

X-ray diffraction
3.34Å resolution

Human DNA polymerase kappa extending opposite a cis-syn thymine dimer

Released:
DOI: 10.2210/pdb3pzp/pdb
PDB entry 3pzp coloured by chain, front view.
PDB entry 3pzp coloured by chain, side view.
PDB entry 3pzp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Role of human DNA polymerase κ in extension opposite from a cis-syn thymine dimer.
Vasquez-Del Carpio R, Silverstein TD, Lone S, Johnson RE, Prakash L, Prakash S, Aggarwal AK
J Mol Biol 408 252-61 (2011)
PMID: 21354175

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-116726 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase kappa Chains: A, B
Molecule details ›
Chains: A, B
Length: 517 amino acids
Theoretical weight: 58.9 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q9UBT6 (Residues: 19-528; Coverage: 59%)
Gene names: DINB1, POLK
Sequence domains:
Structure domains:
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*A)-3' Chains: P, Q
Molecule details ›
Chains: P, Q
Length: 13 nucleotides
Theoretical weight: 4.09 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*TP*TP*CP*CP*(TTD)P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' Chains: T, U
Molecule details ›
Chains: T, U
Length: 17 nucleotides
Theoretical weight: 5.35 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DTP 2 x DTP
Ligand MG 4 x MG
1 modified residue:
Ligand TTD 2 x TTD

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: C2221
Unit cell:
a: 117.136Å b: 154.476Å c: 217.854Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.244 0.242 0.288
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

1 review citation

Mechanisms of mutagenesis: DNA replication in the presence of DNA damage.
Liu et al. (2016)
6 other articles

6 mentions without citation

An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η.
Yang W. (2014)
5 more