5E8F

Structure of Fully modified geranylgeranylated PDE6C Peptide in complex with PDE6D

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5e8fa_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	RhoGDI-like	GMP-PDE delta	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d5e8fc_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	RhoGDI-like	GMP-PDE delta	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	E set domains	8055021	3000070	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	E set domains	8055021	3000070	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	GMP_PDE_delta	e5e8fA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: GMP_PDE_delta	ECOD (1.6)
B [auth C]	GMP_PDE_delta	e5e8fC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: GMP_PDE_delta	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.70.50.40	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)
B [auth C]	2.70.50.40	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C]	PF05351	GMP-PDE, delta subunit (GMP_PDE_delta)	GMP-PDE, delta subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], D [auth E]	Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'	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 organic cyclic compound 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	detection of light stimulus response to light stimulus phototransduction cellular response to stimulus detection of external stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation detection of visible light response to external stimulus detection of abiotic stimulus cell communication detection of stimulus detection of light stimulus response to light stimulus phototransduction cellular response to stimulus detection of external stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation detection of visible light response to external stimulus detection of abiotic stimulus cell communication detection of stimulus response to abiotic stimulus response to radiation cellular process signal transduction phototransduction, visible light multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception intracellular signal transduction cAMP-mediated signaling intracellular signaling cassette 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	cell periphery plasma membrane membrane cellular anatomical entity
A, B [auth C]	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	GTPase regulator activity enzyme regulator activity GTPase inhibitor activity molecular function inhibitor activity nucleoside-triphosphatase regulator activity molecular function regulator activity enzyme inhibitor activity small GTPase binding protein binding binding enzyme binding GTPase binding	multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane cell projection cilium plasma membrane bounded cell projection cytoskeleton intracellular non-membrane-bounded organelle non-membrane-bounded organelle cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D], D [auth E]	IPR003607	HD/PDEase domain	Domain
C [auth D], D [auth E]	IPR002073	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	Domain
C [auth D], D [auth E]	IPR036971	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR003018	GAF domain	Domain
C [auth D], D [auth E]	IPR029016	GAF-like domain superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR023088	3'5'-cyclic nucleotide phosphodiesterase	Family
C [auth D], D [auth E]	IPR023174	3'5'-cyclic nucleotide phosphodiesterase, conserved site	Conserved Site
A, B [auth C]	IPR008015	GMP phosphodiesterase, delta subunit	Domain
A, B [auth C]	IPR017287	Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit	Family
A, B [auth C]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B [auth C]	IPR037036	GMP phosphodiesterase, delta subunit superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth D], D [auth E]	Pharos: P51160	achromatopsia cone dystrophy 4 cone dystrophy amphetamine abuse Amphetamine Addiction cone-rod dystrophy atrial fibrillation
A, B [auth C]	Pharos: O43924	orofaciodigital syndrome type 6 Joubert syndrome 22 atrial fibrillation Ciliopathies ovarian cancer breast cancer coloboma Sjogren syndrome Joubert syndrome polydactyly

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth D], D [auth E]	CMT	Parent Component: CYS RESID: AA0105 PSI-MOD : L-cysteine methyl ester MOD:00114

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.