› 2w4i

X-ray diffraction
1.87Å resolution

Crystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate and an inhibitor

Released:
DOI: 10.2210/pdb2w4i/pdb
PDB entry 2w4i coloured by chain, front view.
PDB entry 2w4i coloured by chain, side view.
PDB entry 2w4i coloured by chain, top view.
Source organism: Helicobacter pylori
Primary publication:
Potent and selective inhibitors of Helicobacter pylori glutamate racemase (MurI): pyridodiazepine amines.
Geng B, Basarab G, Comita-Prevoir J, Gowravaram M, Hill P, Kiely A, Loch J, MacPherson L, Morningstar M, Mullen G, Osimboni E, Satz A, Eyermann C, Lundqvist T
Bioorg Med Chem Lett 19 930-6 (2009)
PMID: 19097892

Function and Biology Details

Reaction catalysed: 
L-glutamate = D-glutamate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195675 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glutamate racemase Chains: A, B, E, F
Molecule details ›
Chains: A, B, E, F
Length: 255 amino acids
Theoretical weight: 28.53 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9ZLT0 (Residues: 1-255; Coverage: 100%)
Gene names: glr, jhp_0496, murI
Sequence domains: Asp/Glu/Hydantoin racemase
Structure domains: Rossmann fold

Ligands and Environments

2 bound ligands:
Ligand DGL 4 x DGL
Ligand VGA 2 x VGA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I711
Spacegroup: P21
Unit cell:
a: 59.074Å b: 93.982Å c: 101.295Å
α: 90° β: 91.46° γ: 90°
R-values:
R R work R free
0.158 0.156 0.209
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Challenges of antibacterial discovery.
Silver LL. (2011)
6 more

3 mentions without citation

Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations.
Whalen et al. (2013)
2 more