› 5w2a

X-ray diffraction
2.9Å resolution

Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dCMPNPP

Released:
DOI: 10.2210/pdb5w2a/pdb
PDB entry 5w2a coloured by chain, front view.
PDB entry 5w2a coloured by chain, side view.
PDB entry 5w2a coloured by chain, top view.
Source organisms:
Primary publication:
Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase κ.
Yockey OP, Jha V, Ghodke PP, Xu T, Xu W, Ling H, Pradeepkumar PI, Zhao L
Chem Res Toxicol 30 2023-2032 (2017)
PMID: 28972744

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-119319 (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*GP*CP*GP*GP*AP*TP*CP*AP*G)-3') Chains: C, P
Molecule details ›
Chains: C, P
Length: 9 nucleotides
Theoretical weight: 2.78 KDa
Source organism: unidentified
Expression system: Not provided
DNA (5'-D(*AP*TP*GP*(LDG)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3') Chains: D, T
Molecule details ›
Chains: D, T
Length: 13 nucleotides
Theoretical weight: 4.25 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MG 2 x MG
Ligand GOL 4 x GOL
Ligand 0KX 2 x 0KX
Ligand PGE 2 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 63.891Å b: 129.014Å c: 167.346Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.231 0.27
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

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

2 mentions without citation

2.0 Å resolution crystal structure of human polκ reveals a new catalytic function of N-clasp in DNA replication.
Jha et al. (2018)
1 more