5YX1

Crystal structure of hematopoietic prostaglandin D synthase in complex with U004


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 
    0.216 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UX4Click on this verticalbar to view detailsBest fitted GSHClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Crystal structure of hematopoietic prostaglandin D synthase in complex with U004

Inaka, K.Furubayashi, N.Kamo, M.Aritake, K.Urade, Y.Takaya, D.Tanaka, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hematopoietic prostaglandin D synthase
A, B, C, D
198Homo sapiensMutation(s): 0 
Gene Names: HPGDSGSTSPGDSPTGDS2
EC: 5.3.99.2 (PDB Primary Data), 2.5.1.18 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60760 (Homo sapiens)
Explore O60760 
Go to UniProtKB:  O60760
PHAROS:  O60760
GTEx:  ENSG00000163106 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60760
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UX4
Query on UX4

Download Ideal Coordinates CCD File 
H [auth B],
L [auth C],
N [auth D]
ethyl 4-[(8R)-3,8-dimethyl-4-oxo-4,6,7,8,9,10-hexahydrothieno[2',3':4,5]pyrimido[1,2-a]azepin-2-yl]carbamoylpiperazine-1-carboxylate
C21 H29 N5 O4 S
XBHQVTSPEFNYKC-CYBMUJFWSA-N
GSH
Query on GSH

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B],
K [auth C],
M [auth D]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth B],
O [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
J [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.447α = 92.2
b = 47.119β = 98.67
c = 91.924γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UX4Click on this verticalbar to view detailsBest fitted GSHClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description