1PD2

CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPLEX WITH GLUTATHIONE

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth 2]	d1pd221	All alpha proteins	GST C-terminal domain-like	GST C-terminal domain-like	Glutathione S-transferase (GST), C-terminal domain	Class sigma GST	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B [auth 2]	d1pd222	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione S-transferase (GST), N-terminal domain	Class sigma GST	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A [auth 1]	d1pd211	All alpha proteins	GST C-terminal domain-like	GST C-terminal domain-like	Glutathione S-transferase (GST), C-terminal domain	Class sigma GST	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A [auth 1]	d1pd212	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione S-transferase (GST), N-terminal domain	Class sigma GST	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth 2]	SCOP2B Superfamily	Thioredoxin-like	8044375	3000031	SCOP2B (2022-06-29)
B [auth 2]	SCOP2B Superfamily	GST C-terminal domain-like	8037548	3000305	SCOP2B (2022-06-29)
A [auth 1]	SCOP2 Family	Glutathione S-transferase (GST), C-terminal domain	8025169	4000976	SCOP2 (2022-06-29)
A [auth 1]	SCOP2 Family	Glutathione S-transferase (GST), N-terminal domain	8031997	4000472	SCOP2 (2022-06-29)
A [auth 1]	SCOP2 Superfamily	GST C-terminal domain-like	8037548	3000305	SCOP2 (2022-06-29)
A [auth 1]	SCOP2 Superfamily	Thioredoxin-like	8044375	3000031	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth 2]	GST_C_3	e1pd221	A: alpha superhelices	X: Repetitive alpha hairpins	H: Glutathione S-transferase (GST)-C (From Topology)	T: Glutathione S-transferase (GST)-C	F: GST_C_3	ECOD (1.6)
B [auth 2]	GST_N_5	e1pd222	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: GST_N_5	ECOD (1.6)
A [auth 1]	GST_C_3	e1pd211	A: alpha superhelices	X: Repetitive alpha hairpins	H: Glutathione S-transferase (GST)-C (From Topology)	T: Glutathione S-transferase (GST)-C	F: GST_C_3	ECOD (1.6)
A [auth 1]	GST_N_5	e1pd212	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: GST_N_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth 2]	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B [auth 2]	1.20.1050.10	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
A [auth 1]	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
A [auth 1]	1.20.1050.10	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth 1], B [auth 2]	PF14497	Glutathione S-transferase, C-terminal domain (GST_C_3)	Glutathione S-transferase, C-terminal domain	This domain is closely related to Pfam:PF00043.	Domain
A [auth 1], B [auth 2]	PF02798	Glutathione S-transferase, N-terminal domain (GST_N)	Glutathione S-transferase, N-terminal domain	Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but not GSTs: S-crystallins from squid (similarity to GST previously noted); eukaryotic elongation factors 1-gamma (not known to have GST activity a ...	Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but not GSTs: S-crystallins from squid (similarity to GST previously noted); eukaryotic elongation factors 1-gamma (not known to have GST activity and similarity not previously recognised); HSP26 family of stress-related proteins including auxin-regulated proteins in plants and stringent starvation proteins in E. coli (not known to have GST activity and similarity not previously recognised). The glutathione molecule binds in a cleft between the N- and C-terminal domains - the catalytically important residues are proposed to reside in the N-terminal domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth 1], B [auth 2]	HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding calcium ion binding identical protein binding protein binding protein homodimerization activity protein dimerization activity glutathione transferase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding calcium ion binding identical protein binding protein binding protein homodimerization activity protein dimerization activity glutathione transferase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity isomerase activity intramolecular oxidoreductase activity prostaglandin-D synthase activity	icosanoid metabolic process prostaglandin metabolic process unsaturated fatty acid metabolic process oxoacid metabolic process cellular biosynthetic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process prostanoid metabolic process icosanoid biosynthetic process small molecule metabolic process prostaglandin biosynthetic process prostanoid biosynthetic process icosanoid metabolic process prostaglandin metabolic process unsaturated fatty acid metabolic process oxoacid metabolic process cellular biosynthetic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process prostanoid metabolic process icosanoid biosynthetic process small molecule metabolic process prostaglandin biosynthetic process prostanoid biosynthetic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process primary metabolic process fatty acid biosynthetic process unsaturated fatty acid biosynthetic process biosynthetic process cellular lipid metabolic process metabolic process cellular process monocarboxylic acid metabolic process lipid metabolic process multicellular organismal process negative regulation of male germ cell proliferation regulation of cellular process sexual reproduction regulation of reproductive process reproductive process regulation of male germ cell proliferation negative regulation of biological process gamete generation germ cell proliferation regulation of germ cell proliferation negative regulation of cellular process regulation of multicellular organismal process regulation of biological process negative regulation of cell population proliferation cell population proliferation multicellular organismal reproductive process biological regulation male germ cell proliferation negative regulation of reproductive process regulation of cell population proliferation negative regulation of multicellular organismal process negative regulation of germ cell proliferation	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth 1], B [auth 2]	IPR004046	Glutathione S-transferase, C-terminal	Domain
A [auth 1], B [auth 2]	IPR010987	Glutathione S-transferase, C-terminal-like	Domain
A [auth 1], B [auth 2]	IPR004045	Glutathione S-transferase, N-terminal	Domain
A [auth 1], B [auth 2]	IPR050213	Glutathione S-transferase superfamily	Family
A [auth 1], B [auth 2]	IPR036282	Glutathione S-transferase, C-terminal domain superfamily	Homologous Superfamily
A [auth 1], B [auth 2]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A [auth 1], B [auth 2]	IPR040079	Glutathione transferase family	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A [auth 1]	prostaglandin-D synthase M-CSA #719	Hematopoietic prostaglandin-D synthase (H-PGDS) is a homodimer in an asymmetric unit. Each monomer is complexed with one glutathione (GTT or GSH) molecule. H-PGDS is one of two types of prostaglandin-D synthase (PGDS) that catalyses the isomerisation of PGH2 to PGD2. PGD2 is a lipid mediator produced by a variety of cells of the immune system, including Th2 and mast cells, that accelerates allergic and inflammatory responses, regulates body temperature, inhibits platelet aggregation, promotes sleep and numerous other physiological functions. H-PGDS is also a member of the glutathione S-transferase (GST) gene family, a group of enzymes that catalyse the conjugation of GSH to an electrophilic substrate.	Defined by 3 residues: TYR:A-8 [auth 1-8]ARG:A-14 [auth 1-14]TRP:A-104 [auth 1-104] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 5.3.99.2 (PDB Primary Data) Search M-CSA Motif + EC 5.3.99.2 EC: 2.5.1.18 (UniProt) Search M-CSA Motif + EC 2.5.1.18

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.