› 3hw8

X-ray diffraction
1.95Å resolution

ternary complex of DNA polymerase lambda of a two nucleotide gapped DNA substrate with a C in the scrunch site

Released:
DOI: 10.2210/pdb3hw8/pdb
PDB entry 3hw8 coloured by chain, front view.
PDB entry 3hw8 coloured by chain, side view.
PDB entry 3hw8 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Garcia-Diaz M, Bebenek K, Larrea AA, Havener JM, Perera L, Krahn JM, Pedersen LC, Ramsden DA, Kunkel TA

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-116380 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase lambda Chain: A
Molecule details ›
Chain: A
Length: 335 amino acids
Theoretical weight: 37.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UGP5 (Residues: 242-575; Coverage: 58%)
Gene name: POLL
Sequence domains:
Structure domains:
5'-D(*CP*GP*GP*CP*CP*AP*AP*TP*AP*CP*TP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*CP*AP*GP*TP*AP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: Homo sapiens
Expression system: Not provided
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

4 bound ligands:
Ligand MG 1 x MG
Ligand NA 4 x NA
Ligand D3T 1 x D3T
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 56.249Å b: 68.386Å c: 137.108Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.212 0.233
Expression systems:
  • Escherichia coli
  • Not provided

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