3JAB | pdb_00003jab

Domain organization and conformational plasticity of the G protein effector, PDE6

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth O]	SCOP2B Superfamily	HD-domain/PDEase-like	8067453	3000943	SCOP2B (2022-06-29)
E [auth C]	SCOP2 Family	PDEase-like	8067452	4001423	SCOP2 (2022-06-29)
E [auth C]	SCOP2 Superfamily	HD-domain/PDEase-like	8067453	3000943	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth Q]	e3jabQ1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: SusG_C	F:	ECOD (20:10:01)
L [auth Q]	e3jabQ2	A: Lipocalins/Streptavidin	X: SAM/DNA-glycosylase	H: SAM domain-like	T: EF-hand_1, EF-hand_6, EF-hand_7	F:	ECOD (20:10:01)
J [auth H]	e3jabH1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: SusG_C	F:	ECOD (20:10:01)
J [auth H]	e3jabH2	A: Lipocalins/Streptavidin	X: SAM/DNA-glycosylase	H: SAM domain-like	T: EF-hand_1, EF-hand_6, EF-hand_7	F:	ECOD (20:10:01)
K [auth R]	e3jabR1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: SusG_C	F:	ECOD (20:10:01)
I [auth L]	e3jabL1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: SusG_C	F:	ECOD (20:10:01)
G [auth O]	e3jabO1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: SusG_C	F:	ECOD (20:10:01)
E [auth C]	e3jabC1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: SusG_C	F:	ECOD (20:10:01)
D [auth N]	e3jabN1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: SusG_C	F:	ECOD (20:10:01)
C [auth B]	e3jabB1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: SusG_C	F:	ECOD (20:10:01)
B [auth M]	e3jabM1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: SusG_C	F:	ECOD (20:10:01)
A	e3jabA1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: SusG_C	F:	ECOD (20:10:01)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
J [auth H], L [auth Q]	2E8 Fab	VH-CH1	Mus musculus (house mouse)	IGHV14-402, IGHJ301, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)
I [auth L], K [auth R]	2E8 Fab	L-KAPPA	Mus musculus (house mouse)	IGKV6-1301, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
J [auth H], L [auth Q]	Heavy Chain	IGHV14	-	phosphodiesterase 5/6 chimera catalytic domain	SAbDab (2026-03-13)
I [auth L], K [auth R]	Light Chain	IGKV6	Kappa	phosphodiesterase 5/6 chimera catalytic domain	SAbDab (2026-03-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth C], G [auth O]	PF00233	3'5'-cyclic nucleotide phosphodiesterase (PDEase_I)	3'5'-cyclic nucleotide phosphodiesterase		Domain
C [auth B], D [auth N]	PF01590	GAF domain (GAF)	GAF domain	This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regul ...	This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J [auth H], L [auth Q]	IgG1-kappa 2E8 heavy chain	-	-	-
I [auth L], K [auth R]	IgG1-kappa 2E8 light chain	-	-	-
F [auth D], H [auth P]	phosphodiesterase 6 gamma subunit inhibitory peptide	molecular adaptor activity cation binding transition metal ion binding zinc ion 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 molecular adaptor activity cation binding transition metal ion binding zinc ion 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-GMP phosphodiesterase activity guanyl nucleotide binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding cGMP binding	cellular response to stimulus positive regulation of cell communication regulation of biological process regulation of signaling regulation of cellular process positive regulation of signal transduction response to stimulus signaling biological regulation positive regulation of biological process regulation of signal transduction positive regulation of G protein-coupled receptor signaling pathway cell communication positive regulation of response to stimulus regulation of response to stimulus cellular response to stimulus positive regulation of cell communication regulation of biological process regulation of signaling regulation of cellular process positive regulation of signal transduction response to stimulus signaling biological regulation positive regulation of biological process regulation of signal transduction positive regulation of G protein-coupled receptor signaling pathway cell communication positive regulation of response to stimulus regulation of response to stimulus regulation of cell communication G protein-coupled receptor signaling pathway cellular process signal transduction regulation of G protein-coupled receptor signaling pathway positive regulation of cellular process positive regulation of signaling intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade cell surface receptor protein tyrosine kinase signaling pathway positive regulation of ERBB signaling pathway regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of epidermal growth factor receptor signaling pathway regulation of ERBB signaling pathway cell surface receptor signaling pathway ERBB signaling pathway multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception	membrane-bounded organelle non-motile cilium membrane plasma membrane cilium 9+0 non-motile cilium neuron projection ciliary membrane photoreceptor outer segment membrane photoreceptor outer segment plasma membrane bounded cell projection cell periphery cell projection bounding membrane of organelle membrane-bounded organelle non-motile cilium membrane plasma membrane cilium 9+0 non-motile cilium neuron projection ciliary membrane photoreceptor outer segment membrane photoreceptor outer segment plasma membrane bounded cell projection cell periphery cell projection bounding membrane of organelle cellular anatomical structure photoreceptor cell cilium organelle plasma membrane region organelle membrane cell projection membrane photoreceptor disc membrane
E [auth C], G [auth O]	phosphodiesterase 5/6 chimera catalytic domain	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 multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception 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	membrane-bounded organelle non-motile cilium membrane plasma membrane cilium 9+0 non-motile cilium neuron projection ciliary membrane photoreceptor outer segment membrane photoreceptor outer segment plasma membrane bounded cell projection cell periphery cell projection bounding membrane of organelle membrane-bounded organelle non-motile cilium membrane plasma membrane cilium 9+0 non-motile cilium neuron projection ciliary membrane photoreceptor outer segment membrane photoreceptor outer segment plasma membrane bounded cell projection cell periphery cell projection bounding membrane of organelle cellular anatomical structure photoreceptor cell cilium organelle plasma membrane region organelle membrane cell projection membrane photoreceptor disc membrane
C [auth B], D [auth N]	GafB domain of phosphodiesterase 2A	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'-cGMP-stimulated cyclic-nucleotide 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'-cGMP-stimulated cyclic-nucleotide 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 identical protein binding protein binding protein homodimerization activity protein dimerization activity 3',5'-cyclic-GMP phosphodiesterase activity cation binding metal ion binding	response to peptide response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus response to macrophage colony-stimulating factor cellular response to macrophage colony-stimulating factor stimulus ribose phosphate metabolic process ribonucleotide catabolic process catabolic process organophosphate catabolic process carbohydrate derivative metabolic process nucleoside phosphate catabolic process purine ribonucleoside monophosphate catabolic process response to peptide response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus response to macrophage colony-stimulating factor cellular response to macrophage colony-stimulating factor stimulus ribose phosphate metabolic process ribonucleotide catabolic process catabolic process organophosphate catabolic process carbohydrate derivative metabolic process nucleoside phosphate catabolic process purine ribonucleoside monophosphate catabolic process purine nucleoside monophosphate catabolic process nucleobase-containing compound metabolic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine nucleoside monophosphate metabolic process phosphate-containing compound metabolic process GMP metabolic process small molecule metabolic process ribonucleoside monophosphate catabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside monophosphate metabolic process nucleotide catabolic process nucleoside phosphate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process nucleoside monophosphate catabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process GMP catabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process organophosphate metabolic process metabolic process cellular process purine ribonucleotide metabolic process regulation of defense response regulation of biological process regulation of response to external stimulus defense response biological regulation positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response cyclic nucleotide metabolic process cyclic purine nucleotide metabolic process cyclic nucleotide catabolic process cGMP metabolic process cGMP catabolic process regulation of biosynthetic process regulation of cellular process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cellular response to stimulus negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction negative regulation of receptor guanylyl cyclase signaling pathway negative regulation of cell communication cell communication negative regulation of cellular process receptor guanylyl cyclase signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of cell communication negative regulation of vascular permeability regulation of vascular permeability multicellular organismal process system process circulatory system process vascular process in circulatory system regulation of biological quality blood circulation response to granulocyte macrophage colony-stimulating factor cellular response to granulocyte macrophage colony-stimulating factor stimulus negative regulation of intracellular signal transduction negative regulation of cAMP/PKA signal transduction intracellular signal transduction cAMP/PKA signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of cAMP/PKA signal transduction regulation of cellular component organization regulation of organelle organization cellular component organization organelle organization regulation of mitochondrion organization cellular component organization or biogenesis mitochondrion organization response to mechanical stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus developmental process epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development tissue development epithelial cell differentiation endothelial cell development epithelial cell development cell differentiation establishment of endothelial barrier anatomical structure development positive regulation of vascular permeability negative regulation of G protein-coupled receptor signaling pathway regulation of G protein-coupled receptor signaling pathway adenylate cyclase-activating G protein-coupled receptor signaling pathway negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular response to nitrogen compound response to organophosphorus cellular response to cGMP response to oxygen-containing compound response to nitrogen compound response to cGMP response to purine-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane cell periphery plasma membrane synapse cell junction plasma membrane region synaptic membrane cytosol presynapse presynaptic membrane Golgi apparatus endomembrane system perinuclear region of cytoplasm organelle outer membrane bounding membrane of organelle mitochondrial outer membrane outer membrane membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus endoplasmic reticulum
A, B [auth M]	GafA domain of cone phosphodiesterase 6C	-	-	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 photoreceptor cell cilium organelle organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth D], H [auth P]	IPR006952	Retinal cGMP phosphodiesterase, gamma subunit	Family
F [auth D], H [auth P]	IPR037030	Retinal cGMP phosphodiesterase, gamma subunit superfamily	Homologous Superfamily
E [auth C], G [auth O]	IPR003607	HD/PDEase domain	Domain
E [auth C], G [auth O]	IPR002073	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	Domain
E [auth C], G [auth O]	IPR036971	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily	Homologous Superfamily
E [auth C], G [auth O]	IPR003018	GAF domain	Domain
E [auth C], G [auth O]	IPR029016	GAF-like domain superfamily	Homologous Superfamily
E [auth C], G [auth O]	IPR023088	3'5'-cyclic nucleotide phosphodiesterase	Family
E [auth C], G [auth O]	IPR023174	3'5'-cyclic nucleotide phosphodiesterase, conserved site	Conserved Site
E [auth C], G [auth O]	IPR003607	HD/PDEase domain	Domain
E [auth C], G [auth O]	IPR002073	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	Domain
E [auth C], G [auth O]	IPR036971	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily	Homologous Superfamily
E [auth C], G [auth O]	IPR003018	GAF domain	Domain
E [auth C], G [auth O]	IPR029016	GAF-like domain superfamily	Homologous Superfamily
E [auth C], G [auth O]	IPR023088	3'5'-cyclic nucleotide phosphodiesterase	Family
E [auth C], G [auth O]	IPR023174	3'5'-cyclic nucleotide phosphodiesterase, conserved site	Conserved Site
C [auth B], D [auth N]	IPR036971	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily	Homologous Superfamily
C [auth B], D [auth N]	IPR003018	GAF domain	Domain
C [auth B], D [auth N]	IPR023174	3'5'-cyclic nucleotide phosphodiesterase, conserved site	Conserved Site
C [auth B], D [auth N]	IPR003607	HD/PDEase domain	Domain
C [auth B], D [auth N]	IPR002073	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	Domain
C [auth B], D [auth N]	IPR029016	GAF-like domain superfamily	Homologous Superfamily
C [auth B], D [auth N]	IPR023088	3'5'-cyclic nucleotide phosphodiesterase	Family
A, B [auth M]	IPR003018	GAF domain	Domain
A, B [auth M]	IPR029016	GAF-like domain superfamily	Homologous Superfamily