› 6bs1

X-ray diffraction
3.15Å resolution

Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion

Released:
DOI: 10.2210/pdb6bs1/pdb
PDB entry 6bs1 coloured by chain, front view.
PDB entry 6bs1 coloured by chain, side view.
PDB entry 6bs1 coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for Human DNA Polymerase Kappa to Bypass Cisplatin Intrastrand Cross-Link (Pt-GG) Lesion as an Efficient and Accurate Extender.
Jha V, Ling H
J Mol Biol 430 1577-1589 (2018)
PMID: 29715472

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-119625 (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: 551 amino acids
Theoretical weight: 63.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBT6 (Residues: 1-526; Coverage: 61%)
Gene names: DINB1, POLK
Sequence domains:
Structure domains:
DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3') Chains: C, P
Molecule details ›
Chains: C, P
Length: 9 nucleotides
Theoretical weight: 2.68 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3') Chains: D, T
Molecule details ›
Chains: D, T
Length: 13 nucleotides
Theoretical weight: 4 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MG 6 x MG
Ligand IOD 9 x IOD
Ligand DZ4 2 x DZ4
Ligand CPT 2 x CPT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P212121
Unit cell:
a: 63.8Å b: 127.72Å c: 168.14Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.247 0.244 0.299
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Mammalian DNA Polymerase Kappa Activity and Specificity.
Stern et al. (2019)
4 more