› 4p4m

X-ray diffraction
1.92Å resolution

Crystal structure of Leishmania infantum polymerase beta: Ternary P/T complex

Released:
DOI: 10.2210/pdb4p4m/pdb
PDB entry 4p4m coloured by chain, front view.
PDB entry 4p4m coloured by chain, side view.
PDB entry 4p4m coloured by chain, top view.
Source organisms:
Primary publication:
Structures of the Leishmania infantum polymerase beta.
Mejia E, Burak M, Alonso A, Larraga V, Kunkel TA, Bebenek K, Garcia-Diaz M
DNA Repair (Amst) 18 1-9 (2014)
PMID: 24666693

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117961 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 378 amino acids
Theoretical weight: 42.96 KDa
Source organism: Leishmania infantum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9U6N3 (Residues: 1-376; Coverage: 100%)
Sequence domains:
Structure domains:
DNA (5'-D(*CP*AP*GP*TP*A)-3') Chain: D
Molecule details ›
Chain: D
Length: 5 nucleotides
Theoretical weight: 1.5 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*TP*AP*CP*TP*G)-3') Chain: E
Molecule details ›
Chain: E
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand D3T 1 x D3T
Ligand MG 1 x MG
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P6522
Unit cell:
a: 108.68Å b: 108.68Å c: 151.641Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.165 0.164 0.182
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Molecular and Functional Characteristics of DNA Polymerase Beta-Like Enzymes From Trypanosomatids.
Maldonado et al. (2021)
2 other articles