› 4c5c

X-ray diffraction
1.4Å resolution

The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ADP and D-ala-D-ala

Released:
DOI: 10.2210/pdb4c5c/pdb
PDB entry 4c5c coloured by chain, front view.
PDB entry 4c5c coloured by chain, side view.
PDB entry 4c5c coloured by chain, top view.
Source organism: Escherichia coli K-12
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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139802 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
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:

Ligands and Environments

4 bound ligands:
Ligand ATP 2 x ATP
Ligand DAL 4 x DAL
Ligand MG 7 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: 51.23Å b: 97.8Å c: 110.12Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.18 0.203
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

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

4 mentions without citation

Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine.
Batson et al. (2017)
3 more