› 4edz

X-ray diffraction
2Å resolution

Crystal structure of hH-PGDS with water displacing inhibitor

Released:
DOI: 10.2210/pdb4edz/pdb
PDB entry 4edz coloured by chain, front view.
PDB entry 4edz coloured by chain, side view.
PDB entry 4edz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Investigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): a tale of two waters.
Trujillo JI, Kiefer JR, Huang W, Day JE, Moon J, Jerome GM, Bono CP, Kornmeier CM, Williams ML, Kuhn C, Rennie GR, Wynn TA, Carron CP, Thorarensen A
Bioorg Med Chem Lett 22 3795-9 (2012)
PMID: 22546671

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: 199 amino acids
Theoretical weight: 23.31 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
2 bound ligands:
Ligand 0O5 4 x 0O5
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: I41
Unit cell:
a: 124.468Å b: 124.468Å c: 105.927Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.236
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description.
Spyrakis et al. (2015)
1 more