› 1v40

X-ray diffraction
1.9Å resolution

First Inhibitor Complex Structure of Human Hematopoietic Prostaglandin D Synthase

Released:
DOI: 10.2210/pdb1v40/pdb
PDB entry 1v40 coloured by chain, front view.
PDB entry 1v40 coloured by chain, side view.
PDB entry 1v40 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
First determination of the inhibitor complex structure of human hematopoietic prostaglandin D synthase.
Inoue T, Okano Y, Kado Y, Aritake K, Irikura D, Uodome N, Okazaki N, Kinugasa S, Shishitani H, Matsumura H, Kai Y, Urade Y
J Biochem 135 279-83 (2004)
PMID: 15113825

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: 198 amino acids
Theoretical weight: 23.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60760 (Residues: 2-199; Coverage: 100%)
Gene names: GSTS, HPGDS, PGDS, PTGDS2
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand GSH 4 x GSH
3 bound ligands:
Ligand MG 2 x MG
Ligand O16 4 x O16
Ligand GOL 6 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL40B2
Spacegroup: P1
Unit cell:
a: 47.288Å b: 49.237Å c: 94.526Å
α: 93.25° β: 89.98° γ: 90.01°
R-values:
R R work R free
0.203 0.195 0.215
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Glutathione transferases: new functions.
Oakley AJ. (2005)
10 other articles

1 mention without citation

Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery.
Wakefield et al. (2020)