› 4c5a

X-ray diffraction
1.65Å resolution

The X-ray crystal structures of D-alanyl-D-alanine ligase in complex ADP and D-cycloserine phosphate

Released:
DOI: 10.2210/pdb4c5a/pdb
PDB entry 4c5a coloured by chain, front view.
PDB entry 4c5a coloured by chain, side view.
PDB entry 4c5a coloured by chain, top view.
Source organisms:
Primary publication:
Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine.
Batson S, de Chiara C, Majce V, Lloyd AJ, Gobec S, Rea D, Fülöp V, Thoroughgood CW, Simmons KJ, Dowson CG, Fishwick CWG, de Carvalho LPS, Roper DI
Nat Commun 8 1939 (2017)
PMID: 29208891

Function and Biology Details

Reaction catalysed: 
ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139803 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
D-alanine--D-alanine ligase B Chains: A, B
Molecule details ›
Chains: A, B
Length: 330 amino acids
Theoretical weight: 35.84 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P07862 (Residues: 1-306; Coverage: 100%)
Gene names: JW0090, b0092, ddl, ddlB
Sequence domains:
Structure domains:
PEPTIDE Chain: C
Molecule details ›
Chain: C
Length: 8 amino acids
Theoretical weight: 941 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ADP 2 x ADP
Ligand DS0 2 x DS0
Ligand MG 4 x MG
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 53.79Å b: 97.51Å c: 109.99Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.205 0.237
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

Mechanisms of action of ionic liquids on living cells: the state of the art.
Kumari et al. (2020)
8 more

5 mentions without citation

Targeting Metalloenzymes for Therapeutic Intervention.
Chen et al. (2019)
4 more