› 4efb

X-ray diffraction
2.2Å resolution

Crystal structure of DNA ligase

Released:
DOI: 10.2210/pdb4efb/pdb
PDB entry 4efb coloured by chain, front view.
PDB entry 4efb coloured by chain, side view.
PDB entry 4efb coloured by chain, top view.
Source organism: Enterococcus faecalis
Entry authors: Wei Y, Wang T, Charifson P, Xu W

Function and Biology Details

Reaction catalysed: 
(1a) NAD(+) + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + beta-nicotinamide D-nucleotide
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182853 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase Chain: A
Molecule details ›
Chain: A
Length: 331 amino acids
Theoretical weight: 37.93 KDa
Source organism: Enterococcus faecalis
Expression system: Not provided
UniProt:
  • Canonical: Q837V6 (Residues: 1-324; Coverage: 48%)
Gene names: EF_0722, ligA
Sequence domains: NAD-dependent DNA ligase adenylation domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 2 x SO4
Ligand NMN 1 x NMN
Ligand 0OW 1 x 0OW
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2
Unit cell:
a: 90.13Å b: 86.01Å c: 56.84Å
α: 90° β: 100.87° γ: 90°
R-values:
R R work R free
0.196 0.196 0.277
Expression system: Not provided

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