3T5G

Structure of fully modified farnesylated Rheb 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)
B	d3t5gb_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	RhoGDI-like	GMP-PDE delta	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3t5ga_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	GTP-binding protein RheB	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	E set domains	8055021	3000070	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057364	3002022	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	GMP_PDE_delta	e3t5gB1	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)
A	Ras	e3t5gA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.70.50.40	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF05351	GMP-PDE, delta subunit (GMP_PDE_delta)	GMP-PDE, delta subunit	-	Family
A	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motil ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	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 intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane cell projection cilium plasma membrane bounded cell projection cytoskeleton membraneless organelle intracellular membraneless organelle cytosol
A	GTP-binding protein Rheb	enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding magnesium ion binding metal ion binding GDP binding protein binding kinase binding enzyme binding protein kinase binding protein serine/threonine kinase activator activity pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process cell development regulation of cell differentiation regulation of type B pancreatic cell development epithelial cell differentiation regulation of cell development multicellular organism development pancreas development columnar/cuboidal epithelial cell development cell differentiation anatomical structure development multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process cell development regulation of cell differentiation regulation of type B pancreatic cell development epithelial cell differentiation regulation of cell development multicellular organism development pancreas development columnar/cuboidal epithelial cell development cell differentiation anatomical structure development endocrine pancreas development type B pancreatic cell differentiation system development developmental process regulation of biological process epithelium development glandular epithelial cell development endocrine system development biological regulation animal organ development type B pancreatic cell development tissue development glandular epithelial cell differentiation epithelial cell development cellular process enteroendocrine cell differentiation columnar/cuboidal epithelial cell differentiation nervous system development neurogenesis central nervous system development gliogenesis oligodendrocyte differentiation glial cell differentiation catabolic process macroautophagy autophagy regulation of catabolic process regulation of autophagy regulation of macroautophagy metabolic process process utilizing autophagic mechanism regulation of metabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus positive regulation of cell communication positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of signaling positive regulation of TORC1 signaling regulation of TORC1 signaling TORC1 signaling positive regulation of nervous system development regulation of neurogenesis regulation of gliogenesis positive regulation of gliogenesis regulation of nervous system development positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal process positive regulation of neurogenesis positive regulation of oligodendrocyte differentiation regulation of multicellular organismal development regulation of glial cell differentiation positive regulation of cell development positive regulation of glial cell differentiation positive regulation of multicellular organismal process regulation of oligodendrocyte differentiation cell cycle regulation of cell cycle negative regulation of cold-induced thermogenesis homeostatic process negative regulation of metabolic process negative regulation of biological process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis negative regulation of cellular process temperature homeostasis negative regulation of multicellular organismal process small GTPase-mediated signal transduction intracellular signaling cassette	cellular anatomical structure endomembrane system membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cellular anatomical structure endomembrane system membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane organelle subcompartment intracellular membrane-bounded organelle endoplasmic reticulum subcompartment intracellular organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane vacuolar membrane lytic vacuole vacuole lytic vacuole membrane bounding membrane of organelle lysosomal membrane lysosome Golgi membrane Golgi apparatus protein-containing complex nucleus nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization synapse cell junction asymmetric synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR008015	GMP phosphodiesterase, delta subunit	Domain
B	IPR017287	Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit	Family
B	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B	IPR037036	GMP phosphodiesterase, delta subunit superfamily	Homologous Superfamily
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR005225	Small GTP-binding domain	Domain
A	IPR020849	Small GTPase, Ras-type	Family
A	IPR001806	Small GTPase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: O43924	orofaciodigital syndrome type 6 Joubert syndrome 22 atrial fibrillation Ciliopathies ovarian cancer breast cancer coloboma Sjogren syndrome Joubert syndrome polydactyly
A	Pharos: Q15382	non-small cell lung carcinoma colorectal cancer intellectual disability glaucoma malignant glioma hypertensive disorder medulloblastoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	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.