3N3Z

Crystal structure of PDE9A (E406A) mutant 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)
B	d3n3zb_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, PDE9A	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3n3za_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, PDE9A	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)
B	SCOP2B Superfamily	HD-domain/PDEase-like	8040956	3000943	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HD-domain/PDEase-like	8040956	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)
B	PDEase_I	e3n3zB1	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	e3n3zA1	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)
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	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	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	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 binding metal ion binding small molecule 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 binding metal ion binding small molecule binding identical protein binding protein binding	ribose phosphate metabolic process ribonucleotide catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process cyclic nucleotide metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process ribose phosphate metabolic process ribonucleotide catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process cyclic nucleotide metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleotide catabolic process nucleoside phosphate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process cyclic purine nucleotide metabolic process cellular metabolic process primary metabolic process purine-containing compound catabolic process cyclic nucleotide catabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound catabolic process cGMP metabolic process organophosphate metabolic process cGMP catabolic process metabolic process cellular process purine ribonucleotide metabolic process positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process cell communication long-term synaptic potentiation synaptic signaling positive regulation of long-term synaptic potentiation regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling biological regulation cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation regulation of cell communication positive regulation of signaling cellular response to stimulus response to stimulus signal transduction muscle hypertrophy regulation of muscle adaptation multicellular organismal process system process positive regulation of cardiac muscle hypertrophy regulation of system process striated muscle hypertrophy regulation of muscle system process muscle system process regulation of cardiac muscle hypertrophy regulation of muscle hypertrophy muscle adaptation regulation of response to stimulus positive regulation of muscle hypertrophy cardiac muscle hypertrophy positive regulation of multicellular organismal process regulation of multicellular organismal process intracellular signal transduction cAMP-mediated signaling intracellular signaling cassette negative regulation of cell population proliferation negative regulation of neural precursor cell proliferation cell population proliferation negative regulation of biological process regulation of cell population proliferation negative regulation of cellular process neural precursor cell proliferation regulation of neural precursor cell proliferation	somatodendritic compartment cell body perikaryon neuronal cell body cellular anatomical entity ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane somatodendritic compartment cell body perikaryon neuronal cell body cellular anatomical entity ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell projection membrane intracellular anatomical structure cytoplasm cytosol sarcolemma membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen Golgi apparatus endomembrane system perinuclear region of cytoplasm endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O76083	bipolar disorder erectile dysfunction malignant colon neoplasm oligodendroglioma breast cancer invasive ductal breast carcinoma malignant mesothelioma ovarian cancer breast carcinoma lung cancer medulloblastoma psoriasis

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.