› 6pz3

X-ray diffraction
2.4Å resolution

Polymerase Eta-catalyzed insertion of correct G opposite template cytarabine (AraC) residue

Released:
DOI: 10.2210/pdb6pz3/pdb
PDB entry 6pz3 coloured by chain, front view.
PDB entry 6pz3 coloured by chain, side view.
PDB entry 6pz3 coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase η.
Rechkoblit O, Johnson RE, Buku A, Prakash L, Prakash S, Aggarwal AK
Sci Rep 9 16400 (2019)
PMID: 31704958

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-120476 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase eta Chain: A
Molecule details ›
Chain: A
Length: 435 amino acids
Theoretical weight: 48.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y253 (Residues: 1-432; Coverage: 61%)
Gene names: POLH, RAD30, RAD30A, XPV
Sequence domains:
DNA Primer strand Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA template containing cytarabine (AraC) residue Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand XG4 1 x XG4
Ligand MG 2 x MG
Ligand GOL 1 x GOL
1 modified residue:
Ligand CAR 1 x CAR

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P61
Unit cell:
a: 98.221Å b: 98.221Å c: 81.348Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.176 0.174 0.216
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Targeting and Monitoring Acute Myeloid Leukaemia with Nucleophosmin-1 (NPM1) Mutation.
Chin et al. (2023)
1 more