2VD1

Complex structure of prostaglandin D2 synthase at 2.25A.

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2vd1a1	All alpha proteins	GST C-terminal domain-like	GST C-terminal domain-like	Glutathione S-transferase (GST), C-terminal domain	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2vd1a2	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2vd1b1	All alpha proteins	GST C-terminal domain-like	GST C-terminal domain-like	Glutathione S-transferase (GST), C-terminal domain	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2vd1b2	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2vd1c1	All alpha proteins	GST C-terminal domain-like	GST C-terminal domain-like	Glutathione S-transferase (GST), C-terminal domain	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2vd1c2	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2vd1d1	All alpha proteins	GST C-terminal domain-like	GST C-terminal domain-like	Glutathione S-transferase (GST), C-terminal domain	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2vd1d2	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Thioredoxin-like	8037452	3000031	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GST C-terminal domain-like	8037451	3000305	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GST C-terminal domain-like	8037451	3000305	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thioredoxin-like	8037452	3000031	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thioredoxin-like	8037452	3000031	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GST C-terminal domain-like	8037451	3000305	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GST C-terminal domain-like	8037451	3000305	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thioredoxin-like	8037452	3000031	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	GST_C_3	e2vd1A1	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	GST_N_5	e2vd1A2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: GST_N_5	ECOD (1.6)
B	GST_C_3	e2vd1B1	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	GST_N_5	e2vd1B2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: GST_N_5	ECOD (1.6)
C	GST_C_3	e2vd1C1	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)
C	GST_N_5	e2vd1C2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: GST_N_5	ECOD (1.6)
D	GST_C_3	e2vd1D1	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)
D	GST_N_5	e2vd1D2	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)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
A	1.20.1050.10	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
B	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B	1.20.1050.10	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
C	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
C	1.20.1050.10	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
D	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
D	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, B, C, D	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, B, C, D	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, B, C, D	GLUTATHIONE-REQUIRING 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	behavior multicellular organismal process locomotory behavior icosanoid metabolic process prostaglandin metabolic process unsaturated fatty acid metabolic process oxoacid metabolic 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 behavior multicellular organismal process locomotory behavior icosanoid metabolic process prostaglandin metabolic process unsaturated fatty acid metabolic process oxoacid metabolic 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 carboxylic acid metabolic process primary metabolic process fatty acid biosynthetic process unsaturated fatty acid biosynthetic process biosynthetic process metabolic process cellular process monocarboxylic acid metabolic process lipid metabolic 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 cellular response to stimulus response to stimulus signaling signal transduction cell communication	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004046	Glutathione S-transferase, C-terminal	Domain
A, B, C, D	IPR010987	Glutathione S-transferase, C-terminal-like	Domain
A, B, C, D	IPR004045	Glutathione S-transferase, N-terminal	Domain
A, B, C, D	IPR050213	Glutathione S-transferase superfamily	Family
A, B, C, D	IPR036282	Glutathione S-transferase, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O60760	testicular germ cell tumor Liver Cirrhosis, Experimental liver disease osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia asthma subependymal giant cell astrocytoma cancer glioblastoma kidney neoplasm lung carcinoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma atopic eczema testicular germ cell tumor Liver Cirrhosis, Experimental liver disease osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia asthma subependymal giant cell astrocytoma cancer glioblastoma kidney neoplasm lung carcinoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma atopic eczema testicular cancer Crohn disease invasive ductal breast carcinoma lung adenocarcinoma malignant colon neoplasm medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm psoriasis schizophrenia bipolar disorder ductal breast carcinoma in situ kidney cancer lung cancer malignant glioma

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.