› 5dmp

X-ray diffraction
1.79Å resolution

Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.

Released:
DOI: 10.2210/pdb5dmp/pdb
PDB entry 5dmp coloured by chain, front view.
PDB entry 5dmp coloured by chain, side view.
PDB entry 5dmp coloured by chain, top view.
Source organism: Methanocella paludicola
Primary publication:
Molecular basis for DNA strand displacement by NHEJ repair polymerases.
Bartlett EJ, Brissett NC, Plocinski P, Carlberg T, Doherty AJ
Nucleic Acids Res 44 2173-86 (2016)
PMID: 26405198

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112335 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase D 3'-phosphoesterase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 169 amino acids
Theoretical weight: 19.06 KDa
Source organism: Methanocella paludicola
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D1Z0H7 (Residues: 30-198; Coverage: 85%)
Gene name: MCP_2127
Sequence domains: DNA polymerase Ligase (LigD)

Ligands and Environments

3 bound ligands:
Ligand EDO 7 x EDO
Ligand MG 1 x MG
Ligand VN4 1 x VN4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P3121
Unit cell:
a: 57.07Å b: 57.07Å c: 105.041Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.176 0.174 0.204
Expression system: Escherichia coli BL21(DE3)

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Citations

6 review citations

Molecular Bases of Drug Resistance in Hepatocellular Carcinoma.
Marin et al. (2020)
5 more

3 mentions without citation

LigD: A Structural Guide to the Multi-Tool of Bacterial Non-Homologous End Joining.
Amare et al. (2021)
2 more