1PD2

CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPLEX WITH GLUTATHIONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Cloning and crystal structure of hematopoietic prostaglandin D synthase.

Kanaoka, Y.Ago, H.Inagaki, E.Nanayama, T.Miyano, M.Kikuno, R.Fujii, Y.Eguchi, N.Toh, H.Urade, Y.Hayaishi, O.

(1997) Cell 90: 1085-1095

  • DOI: https://doi.org/10.1016/s0092-8674(00)80374-8
  • Primary Citation of Related Structures:  
    1PD2

  • PubMed Abstract: 

    Hematopoietic prostaglandin (PG) D synthase is the key enzyme for production of the D and J series of prostanoids in the immune system and mast cells. We isolated a cDNA for the rat enzyme, crystallized the recombinant enzyme, and determined the three-dimensional structure of the enzyme complexed with glutathione at 2.3 A resolution. The enzyme is the first member of the sigma class glutathione S-transferase (GST) from vertebrates and possesses a prominent cleft as the active site, which is never seen among other members of the GST family. The unique 3-D architecture of the cleft leads to the putative substrate binding mode and its catalytic mechanism, responsible for the specific isomerization from PGH2 to PGD2.


  • Organizational Affiliation

    Department of Molecular Behavioral Biology, Osaka Bioscience Institute, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEMATOPOIETIC PROSTAGLANDIN D SYNTHASEA [auth 1],
B [auth 2]
199Rattus norvegicusMutation(s): 0 
EC: 5.3.99.2
UniProt
Find proteins for O35543 (Rattus norvegicus)
Go to UniProtKB:  O35543
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.5α = 90
b = 56.5β = 90
c = 233.4γ = 120
Software Package:
Software NamePurpose
WEISdata scaling
ROTAVATAdata reduction
PHASESphasing
X-PLORrefinement
WEISdata reduction
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-13
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-12-14
    Changes: Non-polymer description
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations