› 1xsp

X-ray diffraction
2.2Å resolution

Crystal Structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate

Released:
DOI: 10.2210/pdb1xsp/pdb
PDB entry 1xsp coloured by chain, front view.
PDB entry 1xsp coloured by chain, side view.
PDB entry 1xsp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A closed conformation for the Pol lambda catalytic cycle.
Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA, Pedersen LC
Nat Struct Mol Biol 12 97-8 (2005)
PMID: 15608652

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 domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114828 (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*GP*TP*AP*CP*TP*G)-3' Chain: T
Molecule details ›
Chain: T
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*CP*AP*GP*TP*AP*CP*G)-3' Chain: P
Molecule details ›
Chain: P
Length: 7 nucleotides
Theoretical weight: 2.12 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

2 bound ligands:
Ligand NA 4 x NA
Ligand PPV 1 x PPV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P212121
Unit cell:
a: 55.845Å b: 62.758Å c: 140.72Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.242
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

20 review citations

Nonhomologous DNA end-joining for repair of DNA double-strand breaks.
Pannunzio et al. (2018)
19 more

7 mentions without citation

The X family portrait: structural insights into biological functions of X family polymerases.
Moon et al. (2007)
6 more