› 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
OpenAccess logo 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