› 3pnc

X-ray diffraction
2Å resolution

Ternary crystal structure of a polymerase lambda variant with a GT mispair at the primer terminus and sodium at catalytic metal site

Released:
DOI: 10.2210/pdb3pnc/pdb
PDB entry 3pnc coloured by chain, front view.
PDB entry 3pnc coloured by chain, side view.
PDB entry 3pnc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Replication infidelity via a mismatch with Watson-Crick geometry.
Bebenek K, Pedersen LC, Kunkel TA
Proc Natl Acad Sci U S A 108 1862-7 (2011)
PMID: 21233421

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-116702 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase lambda Chain: A
Molecule details ›
Chain: A
Length: 329 amino acids
Theoretical weight: 36.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UGP5 (Residues: 242-575; Coverage: 57%)
Gene name: POLL
Sequence domains:
Structure domains:
5'-D(*CP*AP*GP*TP*AP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.83 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*CP*GP*GP*CP*CP*TP*TP*AP*CP*TP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.33 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*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

4 bound ligands:
Ligand 1GC 1 x 1GC
Ligand MG 1 x MG
Ligand NA 3 x NA
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 56.161Å b: 62.254Å c: 139.834Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.208 0.236
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Role of tautomerism in RNA biochemistry.
Singh et al. (2015)
5 more

5 mentions without citation

Structure-function studies of DNA polymerase λ.
Bebenek et al. (2014)
4 more