› 5fpo

X-ray diffraction
1.83Å resolution

Structure of Bacterial DNA Ligase with small-molecule ligand 1H- indazol-7-amine (AT4213) in an alternate binding site.

Released:
DOI: 10.2210/pdb5fpo/pdb
PDB entry 5fpo coloured by chain, front view.
PDB entry 5fpo coloured by chain, side view.
PDB entry 5fpo coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Detection of secondary binding sites in proteins using fragment screening.
Ludlow RF, Verdonk ML, Saini HK, Tickle IJ, Jhoti H
Proc Natl Acad Sci U S A 112 15910-5 (2015)
PMID: 26655740

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-189554 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase Chain: A
Molecule details ›
Chain: A
Length: 318 amino acids
Theoretical weight: 36.72 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9AIU7 (Residues: 1-312; Coverage: 47%)
Gene names: lig, ligA
Sequence domains: NAD-dependent DNA ligase adenylation domain
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 10L 3 x 10L
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2
Unit cell:
a: 171.886Å b: 39.66Å c: 48.78Å
α: 90° β: 90.11° γ: 90°
R-values:
R R work R free
0.213 0.211 0.249
Expression system: Escherichia coli BL21(DE3)

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Citations

12 review citations

Twenty years on: the impact of fragments on drug discovery.
Erlanson et al. (2016)
11 more

2 mentions without citation

Detection of secondary binding sites in proteins using fragment screening.
Ludlow et al. (2015)
1 more