3JWQ | pdb_00003jwq

Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with sildenafil

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	d3jwqd_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3jwqc1	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3jwqc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3jwqb_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3jwqa_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ], 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	8042136	3000943	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HD-domain/PDEase-like	8042136	3000943	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HD-domain/PDEase-like	8042136	3000943	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HD-domain/PDEase-like	8042136	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	PDEase_I	e3jwqD1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
C	PDEase_I	e3jwqC1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
B	PDEase_I	e3jwqB1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
A	PTS_IIA	e3jwqA1	A: alpha bundles	X: Spectrin repeat-like	H: Enzyme IIa from lactose specific PTS, IIa-lac	T: Enzyme IIa from lactose specific PTS, IIa-lac	F: PTS_IIA	ECOD (develop294)

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	cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera	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 guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide 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-GMP phosphodiesterase activity guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding cGMP binding small molecule binding 3',5'-cyclic-AMP phosphodiesterase activity cation binding metal ion binding	cellular response to stimulus regulation of cellular process response to stimulus 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 cellular response to stimulus regulation of cellular process response to stimulus 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 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 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 purine ribonucleotide metabolic process detection of light stimulus response to light stimulus phototransduction detection of external stimulus detection of visible light response to external stimulus detection of abiotic stimulus detection of stimulus response to abiotic stimulus response to radiation phototransduction, visible light multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception cellular developmental process sensory organ development photoreceptor cell differentiation visual system development retina development in camera-type eye cell development neural retina development eye morphogenesis multicellular organism development neurogenesis neuron differentiation cell differentiation retinal cone cell differentiation eye photoreceptor cell differentiation anatomical structure development animal organ morphogenesis sensory system development system development photoreceptor cell development developmental process camera-type eye morphogenesis eye development eye photoreceptor cell development animal organ development retinal cone cell development nervous system development camera-type eye photoreceptor cell differentiation generation of neurons retina morphogenesis in camera-type eye anatomical structure morphogenesis sensory organ morphogenesis neuron development camera-type eye development	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle non-motile cilium membrane 9+0 non-motile cilium cilium neuron projection photoreceptor disc membrane photoreceptor outer segment plasma membrane bounded cell projection cell projection cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle non-motile cilium membrane 9+0 non-motile cilium cilium neuron projection photoreceptor disc membrane photoreceptor outer segment plasma membrane bounded cell projection cell projection photoreceptor cell cilium organelle organelle membrane cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003607	HD/PDEase 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	IPR003018	GAF domain	Domain
A, B, C, D	IPR029016	GAF-like 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
A, B, C, D	IPR003607	HD/PDEase 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	IPR003018	GAF domain	Domain
A, B, C, D	IPR029016	GAF-like 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: P51160	Neoplasm Metastasis erectile dysfunction malignant pancreatic neoplasm ovarian cancer pituitary cancer atrial fibrillation breast cancer pulmonary hypertension congestive heart failure exocrine pancreatic carcinoma head and neck cancer lung adenocarcinoma malignant ependymoma medulloblastoma non-small cell lung carcinoma Neoplasm Metastasis erectile dysfunction malignant pancreatic neoplasm ovarian cancer pituitary cancer atrial fibrillation breast cancer pulmonary hypertension congestive heart failure exocrine pancreatic carcinoma head and neck cancer lung adenocarcinoma malignant ependymoma medulloblastoma non-small cell lung carcinoma peripheral vascular disease atypical teratoid rhabdoid tumor priapism breast carcinoma type 2 diabetes mellitus diabetes mellitus gastric cancer hypertensive disorder lung cancer malignant mesothelioma osteosarcoma Peyronie disease premature ejaculation benign prostatic hyperplasia pulmonary arterial hypertension ulcerative colitis gastric carcinoma large cell medulloblastoma malignant colon neoplasm achromatopsia cone dystrophy 4 cone dystrophy amphetamine abuse Amphetamine Addiction cone-rod dystrophy 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.