› 2x5o

X-ray diffraction
1.46Å resolution

Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- thiazolidine-2,4-dione Inhibitors of MurD Ligase

Released:
DOI: 10.2210/pdb2x5o/pdb
PDB entry 2x5o coloured by chain, front view.
PDB entry 2x5o coloured by chain, side view.
PDB entry 2x5o coloured by chain, top view.
Source organism: Escherichia coli DH5[alpha]
Primary publication:
Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD ligase.
Zidar N, Tomasić T, Sink R, Rupnik V, Kovac A, Turk S, Patin D, Blanot D, Contreras Martel C, Dessen A, Müller Premru M, Zega A, Gobec S, Peterlin Masic L, Kikelj D
J Med Chem 53 6584-94 (2010)
PMID: 20804196

Function and Biology Details

Reaction catalysed: 
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147132 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UDP-N-acetylmuramoylalanine--D-glutamate ligase Chain: A
Molecule details ›
Chain: A
Length: 439 amino acids
Theoretical weight: 47.16 KDa
Source organism: Escherichia coli DH5[alpha]
Expression system: Escherichia coli DH5[alpha]
UniProt:
  • Canonical: P14900 (Residues: 2-438; Coverage: 100%)
Gene names: JW0086, b0088, murD
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand VSV 1 x VSV
Ligand AZI 1 x AZI
Ligand SO4 2 x SO4
Ligand SO3 1 x SO3
Ligand CL 4 x CL
1 modified residue:
Ligand KCX 1 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P41
Unit cell:
a: 66.091Å b: 66.091Å c: 135.781Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.185 0.217
Expression system: Escherichia coli DH5[alpha]

Quick links

Citations

10 review citations

Resistance to antibiotics targeted to the bacterial cell wall.
Nikolaidis et al. (2014)
9 more

5 mentions without citation

Recent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches.
Gaur et al. (2022)
4 more