› 4u7c

X-ray diffraction
2.8Å resolution

Structure of DNA polymerase kappa in complex with benzopyrene adducted DNA

Released:
DOI: 10.2210/pdb4u7c/pdb
PDB entry 4u7c coloured by chain, front view.
PDB entry 4u7c coloured by chain, side view.
PDB entry 4u7c coloured by chain, top view.
Source organisms:
Primary publication:
Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase κ.
Jha V, Bian C, Xing G, Ling H
Nucleic Acids Res 44 4957-67 (2016)
PMID: 27034468

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-118182 (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: 492 amino acids
Theoretical weight: 56.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9UBT6 (Residues: 27-518; Coverage: 57%)
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(*P*AP*TP*GP*(VKJ)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3') Chains: D, T
Molecule details ›
Chains: D, T
Length: 13 nucleotides
Theoretical weight: 4.27 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MG 2 x MG
Ligand 0KX 2 x 0KX
Ligand PEG 3 x PEG
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P212121
Unit cell:
a: 63.64Å b: 130.17Å c: 166.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.212 0.252
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

7 review citations

Mechanisms of DNA damage, repair, and mutagenesis.
Chatterjee et al. (2017)
6 more

4 mentions without citation

Translesion Synthesis: Insights into the Selection and Switching of DNA Polymerases.
Zhao et al. (2017)
3 more