1SOJ | pdb_00001soj

CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH IBMX

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)
L	d1sojl_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d1sojk_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d1sojj_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d1soji_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d1sojh_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d1sojg_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1sojf_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1soje_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1sojd_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1sojc_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1sojb_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1soja_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b	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)
L	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HD-domain/PDEase-like	8041634	3000943	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)
L	PDEase_I	e1sojL1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
K	PDEase_I	e1sojK1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
J	PDEase_I	e1sojJ1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
I	PDEase_I	e1sojI1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
H	PDEase_I	e1sojH1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
G	PDEase_I	e1sojG1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
F	PDEase_I	e1sojF1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
E	PDEase_I	e1sojE1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
D	PDEase_I	e1sojD1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
C	PDEase_I	e1sojC1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
B	PDEase_I	e1sojB1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
A	PDEase_I	e1sojA1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
K	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
J	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
I	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
H	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
G	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
F	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
E	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
D	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
C	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
B	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
A	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF00233	3'5'-cyclic nucleotide phosphodiesterase (PDEase_I)	3'5'-cyclic nucleotide phosphodiesterase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	cGMP-inhibited 3',5'-cyclic phosphodiesterase B	protein binding binding protein kinase B binding kinase binding enzyme binding protein kinase binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity 3',5'-cyclic-nucleotide phosphodiesterase activity hydrolase activity cyclic-nucleotide phosphodiesterase activity catalytic activity 3',5'-cyclic-AMP phosphodiesterase activity protein binding binding protein kinase B binding kinase binding enzyme binding protein kinase binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity 3',5'-cyclic-nucleotide phosphodiesterase activity hydrolase activity cyclic-nucleotide phosphodiesterase activity catalytic activity 3',5'-cyclic-AMP phosphodiesterase activity 3',5'-cyclic-GMP phosphodiesterase activity cation binding ion binding metal ion binding small molecule binding	developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development regulation of cellular process negative regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell adhesion negative regulation of biological process negative regulation of cell adhesion cell adhesion cell adhesion mediated by integrin negative regulation of cellular process cellular process cellular response to stimulus response to stimulus signaling negative regulation of signaling regulation of signal transduction negative regulation of G protein-coupled receptor signaling pathway negative regulation of cell communication cell communication signal transduction regulation of G protein-coupled receptor signaling pathway regulation of signaling negative regulation of response to stimulus adenylate cyclase-activating G protein-coupled receptor signaling pathway negative regulation of signal transduction negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway regulation of response to stimulus adenylate cyclase-modulating G protein-coupled receptor signaling pathway regulation of cell communication G protein-coupled receptor signaling pathway regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to insulin cellular response to insulin stimulus cellular response to hormone stimulus negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis negative regulation of vasculature development negative regulation of multicellular organismal process negative regulation of catabolic process lipid catabolic process catabolic process regulation of lipid metabolic process negative regulation of metabolic process primary metabolic process regulation of catabolic process regulation of lipid catabolic process regulation of primary metabolic process metabolic process regulation of metabolic process negative regulation of lipid metabolic process negative regulation of lipid catabolic process lipid metabolic process regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR036971	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR023174	3'5'-cyclic nucleotide phosphodiesterase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR003607	HD/PDEase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR002073	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	Pharos: Q13370	polycystic ovary syndrome Platelet Aggregation Inhibition breast carcinoma cutaneous lupus erythematosus invasive ductal breast carcinoma lung carcinoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma tuberculosis atrial fibrillation breast fibroadenoma ductal breast carcinoma in situ large cell medulloblastoma medulloblastoma osteosarcoma polycystic ovary syndrome Platelet Aggregation Inhibition breast carcinoma cutaneous lupus erythematosus invasive ductal breast carcinoma lung carcinoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma tuberculosis atrial fibrillation breast fibroadenoma ductal breast carcinoma in situ large cell medulloblastoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis atypical teratoid rhabdoid tumor interstitial cystitis lung cancer ovarian cancer

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.