5Y9Z

Crystal structure of rat hematopoietic prostaglandin D synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of rat hematopoietic prostaglandin D synthase

Kamo, M.Furubayashi, N.Inaka, K.Tanaka, H.Aritake, K.Urade, Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hematopoietic prostaglandin D synthase
A, B
199Rattus norvegicusMutation(s): 0 
Gene Names: Hpgds (Gsts, Pgds, Ptgds2)
EC: 5.3.99.2
Find proteins for O35543 (Rattus norvegicus)
Go to UniProtKB:  O35543
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GSH
Query on GSH

Download SDF File 
Download CCD File 
A, B
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

Download SDF File 
Download CCD File 
A, B
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.540α = 90.00
b = 79.840β = 90.00
c = 96.600γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
MOSFLMdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release