› 2vcz

X-ray diffraction
1.95Å resolution

Complex structure of prostaglandin D2 synthase at 1.95A.

Released:
DOI: 10.2210/pdb2vcz/pdb
PDB entry 2vcz coloured by chain, front view.
PDB entry 2vcz coloured by chain, side view.
PDB entry 2vcz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Novel prostaglandin D synthase inhibitors generated by fragment-based drug design.
Hohwy M, Spadola L, Lundquist B, Hawtin P, Dahmén J, Groth-Clausen I, Nilsson E, Persdotter S, von Wachenfeldt K, Folmer RH, Edman K
J Med Chem 51 2178-86 (2008)
PMID: 18341273

Function and Biology Details

Reactions catalysed: 
RX + glutathione = HX + R-S-glutathione
(5Z,13E,15S)-9-alpha,11-alpha-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E,15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130086 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Hematopoietic prostaglandin D synthase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 199 amino acids
Theoretical weight: 23.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O60760 (Residues: 1-199; Coverage: 100%)
Gene names: GSTS, HPGDS, PGDS, PTGDS2
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand GSH 4 x GSH
1 bound ligand:
Ligand VC3 1 x VC3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: I41
Unit cell:
a: 123.429Å b: 123.429Å c: 106.273Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.198 0.246
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

Enzymes of the cyclooxygenase pathways of prostanoid biosynthesis.
Smith et al. (2011)
8 more

2 mentions without citation

Binding mode information improves fragment docking.
Jacquemard et al. (2019)
1 more