› 3mda

X-ray diffraction
2.03Å resolution

DNA polymerase lambda in complex with araC

Released:
DOI: 10.2210/pdb3mda/pdb
PDB entry 3mda coloured by chain, front view.
PDB entry 3mda coloured by chain, side view.
PDB entry 3mda coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Interaction between DNA Polymerase lambda and anticancer nucleoside analogs.
Garcia-Diaz M, Murray MS, Kunkel TA, Chou KM
J Biol Chem 285 16874-9 (2010)
PMID: 20348107

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116558 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase lambda Chain: A
Molecule details ›
Chain: A
Length: 325 amino acids
Theoretical weight: 36.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UGP5 (Residues: 252-575; Coverage: 56%)
Gene name: POLL
Sequence domains:
Structure domains:
DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 11 nucleotides
Theoretical weight: 3.39 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*CP*AP*GP*TP*AP*CP*(CAR))-3') Chain: P
Molecule details ›
Chain: P
Length: 7 nucleotides
Theoretical weight: 2.1 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*GP*CP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand PPV 1 x PPV
Ligand NA 2 x NA
Ligand MG 1 x MG
1 modified residue:
Ligand CAR 1 x CAR

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 56.068Å b: 62.637Å c: 140.163Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.197 0.259
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

Unlocking the sugar "steric gate" of DNA polymerases.
Brown et al. (2011)
7 more

5 mentions without citation

Recent advances in the structural and molecular biology of type IV secretion systems.
Trokter et al. (2014)
4 more