3T5I | pdb_00003t5i

Structure of Fully modified farnesylated Rheb 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)
D	d3t5id_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	RhoGDI-like	GMP-PDE delta	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3t5ic_	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 A]	d3t5ia_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	RhoGDI-like	GMP-PDE delta	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth B]	d3t5ib_	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)
D	SCOP2B Superfamily	E set domains	8055021	3000070	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	E set domains	8055021	3000070	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	E set domains	8055021	3000070	SCOP2B (2022-06-29)
A [auth B]	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)
D	Pkinase, APH	e3t5iD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Pkinase, APH	ECOD (v294.1)
C	Pkinase, APH	e3t5iC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Pkinase, APH	ECOD (v294.1)
B [auth A]	Pkinase, APH	e3t5iA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Pkinase, APH	ECOD (v294.1)
A [auth B]	Pkinase, APH	e3t5iB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Pkinase, APH	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.70.50.40	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)
C	2.70.50.40	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)
B [auth A]	2.70.50.40	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)
A [auth B]	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 [auth B], B [auth A], C, D	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
E [auth Q], F [auth R]	C-terminal Farnesylated Rheb peptide CSQQGKSS(CMT)	-	-	-
A [auth B], B [auth A], C, D	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 cytosol cell projection cilium plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C, D	IPR017287	Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit	Family
A [auth B], B [auth A], C, D	IPR008015	GMP phosphodiesterase, delta subunit	Domain
A [auth B], B [auth A], C, D	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR037036	GMP phosphodiesterase, delta subunit superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], B [auth A], C, D	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
E [auth Q], F [auth R]	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.