› 5ywx

X-ray diffraction
1.74Å resolution

Crystal structure of hematopoietic prostaglandin D synthase in complex with F092

Released:
DOI: 10.2210/pdb5ywx/pdb
PDB entry 5ywx coloured by chain, front view.
PDB entry 5ywx coloured by chain, side view.
PDB entry 5ywx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies.
Takaya D, Inaka K, Omura A, Takenuki K, Kawanishi M, Yabuki Y, Nakagawa Y, Tsuganezawa K, Ogawa N, Watanabe C, Honma T, Aritake K, Urade Y, Shirouzu M, Tanaka A
Bioorg Med Chem 26 4726-4734 (2018)
PMID: 30121213

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 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: 23.24 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 93C 4 x 93C
Ligand GOL 3 x GOL
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P1
Unit cell:
a: 47.04Å b: 48.17Å c: 92.11Å
α: 98.97° β: 92.34° γ: 90.01°
R-values:
R R work R free
0.206 0.203 0.253
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Anti-Inflammatory, Thrombolytic and Hair-Growth Promoting Activity of the n-Hexane Fraction of the Methanol Extract of Leea indica Leaves.
Sakib et al. (2021)
1 more

2 mentions without citation

Development of a Hematopoietic Prostaglandin D Synthase-Degradation Inducer.
Yokoo et al. (2021)
1 more