5Y9Z | pdb_00005y9z

Crystal structure of rat hematopoietic prostaglandin D synthase

PDB DOI: https://doi.org/10.2210/pdb5Y9Z/pdb

Classification: TRANSFERASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-08-29 Released: 2018-09-19
Deposition Author(s): Kamo, M., Furubayashi, N., Inaka, K., Tanaka, H., Aritake, K., Urade, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free:
0.179 (Depositor), 0.185 (DCC)
R-Value Work:
0.155 (Depositor), 0.165 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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.

Macromolecule Content

Total Structure Weight: 48.3 kDa
Atom Count: 3,911
Modeled Residue Count: 396
Deposited Residue Count: 398
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hematopoietic prostaglandin D synthase	A, B	199	Rattus norvegicus	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
Find proteins for O35543 (Rattus norvegicus) Explore O35543 Go to UniProtKB: O35543
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O35543
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A]	C [auth A], L [auth B]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B]	O [auth B], P [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain O [auth B] Focus chain P [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
DIO Query on DIO Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], M [auth B], N [auth B]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	C [auth A], L [auth B]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free: 0.179 (Depositor), 0.185 (DCC)
R-Value Work: 0.155 (Depositor), 0.165 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.54	α = 90
b = 79.84	β = 90
c = 96.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data collection
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-09-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-09-19
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description