5YX1

Crystal structure of hematopoietic prostaglandin D synthase in complex with U004

• PDB DOI: https://doi.org/10.2210/pdb5YX1/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-01 Released: 2018-12-05 
• Deposition Author(s): Kamo, M., Furubayashi, N., Inaka, K., Aritake, K., Urade, Y., Takaya, D., Tanaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.216 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 95.76 kDa 
• Atom Count: 7,634 
• Modelled Residue Count: 792 
• Deposited Residue Count: 792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hematopoietic prostaglandin D synthase	A, B, C, D	198	Homo sapiens	Mutation(s): 0  Gene Names: HPGDS, GSTS, PGDS, PTGDS2 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UX4	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	F [auth A], G [auth B], K [auth C], M [auth D]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
GOL	I [auth B], O [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	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 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.447	α = 92.2
b = 47.119	β = 98.67
c = 91.924	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-05 
Deposition Author(s): Kamo, M., Furubayashi, N., Inaka, K., Aritake, K., Urade, Y., Takaya, D., Tanaka, A.

Revision History  

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