5B25 | pdb_00005b25

Crystal structure of human PDE1B with inhibitor 3

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)
D	d5b25d_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5b25c_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5b25b_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5b25a_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	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)
D	SCOP2B Superfamily	HD-domain/PDEase-like	8040115	3000943	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HD-domain/PDEase-like	8040115	3000943	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HD-domain/PDEase-like	8040115	3000943	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HD-domain/PDEase-like	8040115	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)
D	FtsJ	e5b25D1	A: a/b three-layered sandwiches	X: HhH/H2TH	H: Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein	T: Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein	F: FtsJ	ECOD (v294.1)
C	FtsJ	e5b25C1	A: a/b three-layered sandwiches	X: HhH/H2TH	H: Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein	T: Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein	F: FtsJ	ECOD (v294.1)
B	FtsJ	e5b25B1	A: a/b three-layered sandwiches	X: HhH/H2TH	H: Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein	T: Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein	F: FtsJ	ECOD (v294.1)
A	FtsJ	e5b25A1	A: a/b three-layered sandwiches	X: HhH/H2TH	H: Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein	T: Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein	F: FtsJ	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	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	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B	calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity 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-GMP phosphodiesterase activity protein binding binding calmodulin binding calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity 3',5'-cyclic-AMP phosphodiesterase activity calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity 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-GMP phosphodiesterase activity protein binding binding calmodulin binding calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity 3',5'-cyclic-AMP phosphodiesterase activity cation binding ion binding metal ion binding small molecule binding	response to peptide response to granulocyte macrophage colony-stimulating factor response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus cellular response to granulocyte macrophage colony-stimulating factor stimulus cellular response to stimulus regulation of cellular process signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction response to peptide response to granulocyte macrophage colony-stimulating factor response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus cellular response to granulocyte macrophage colony-stimulating factor stimulus cellular response to stimulus regulation of cellular process signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction negative regulation of cAMP/PKA signal transduction intracellular signal transduction negative regulation of cell communication cell communication cAMP/PKA signal transduction regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of biological process regulation of signaling negative regulation of response to stimulus biological regulation negative regulation of signal transduction regulation of cAMP/PKA signal transduction regulation of response to stimulus regulation of cell communication cellular process behavior multicellular organismal process locomotory behavior response to macrophage colony-stimulating factor cellular response to macrophage colony-stimulating factor stimulus developmental process myeloid leukocyte differentiation cellular developmental process hemopoiesis cell development mononuclear cell differentiation myeloid cell differentiation cell differentiation anatomical structure development monocyte differentiation leukocyte differentiation response to amine response to nitrogen compound response to amphetamine response to light stimulus system process learning learning or memory nervous system process visual learning visual behavior cognition associative learning response to radiation response to abiotic stimulus catecholamine catabolic process catabolic process catechol-containing compound catabolic process dopamine metabolic process catechol-containing compound metabolic process biogenic amine catabolic process phenol-containing compound catabolic process amine metabolic process dopamine catabolic process catecholamine metabolic process phenol-containing compound metabolic process metabolic process biogenic amine metabolic process amine catabolic process serotonin metabolic process indole-containing compound metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell body neuronal cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003607	HD/PDEase domain	Domain
A, B, C, D	IPR013706	PDE1, N-terminal domain	Domain
A, B, C, D	IPR002073	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	Domain
A, B, C, D	IPR036971	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily	Homologous Superfamily
A, B, C, D	IPR023088	3'5'-cyclic nucleotide phosphodiesterase	Family
A, B, C, D	IPR023174	3'5'-cyclic nucleotide phosphodiesterase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q01064	Adult Learning Disorders depressive disorder learning disability MALT lymphoma atrial fibrillation

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.