3DPY

Protein farnesyltransferase complexed with FPP and caged TKCVIM substrate

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3dpya1	All alpha proteins	alpha-alpha superhelix	Protein prenylyltransferase	Protein prenylyltransferase	Protein farnesyltransferase alpha-subunit	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d3dpyb1	All alpha proteins	alpha/alpha toroid	Terpenoid cyclases/Protein prenyltransferases	Protein prenyltransferases	Protein farnesyltransferase, beta-subunit	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Protein prenylyltransferase	8038634	3001312	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Terpenoid cyclases/Protein prenyltransferases	8038407	3001024	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	PPTA	e3dpyA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PPTA	ECOD (1.6)
B	SQHop_cyclase_C	e3dpyB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: SQHop_cyclase_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.40.120	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Protein prenylyltransferase	CATH (4.3.0)
B	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01239	Protein prenyltransferase alpha subunit repeat (PPTA)	Protein prenyltransferase alpha subunit repeat	-	Repeat
B	PF00432	Prenyltransferase alpha-alpha toroid domain (Prenyltrans)	Prenyltransferase and squalene oxidase repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha	catalytic activity, acting on a protein protein geranylgeranyltransferase activity protein prenyltransferase activity prenyltransferase activity transferase activity catalytic activity transferase activity, transferring alkyl or aryl (other than methyl) groups cytoskeletal protein binding protein binding binding tubulin binding alpha-tubulin binding microtubule binding Rab geranylgeranyltransferase activity catalytic activity, acting on a protein protein geranylgeranyltransferase activity protein prenyltransferase activity prenyltransferase activity transferase activity catalytic activity transferase activity, transferring alkyl or aryl (other than methyl) groups cytoskeletal protein binding protein binding binding tubulin binding alpha-tubulin binding microtubule binding Rab geranylgeranyltransferase activity molecular adaptor activity protein farnesyltransferase activity protein tyrosine kinase binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding CAAX-protein geranylgeranyltransferase activity	regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction response to stimulus regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling Rac protein signal transduction positive regulation of intracellular signal transduction regulation of Rac protein signal transduction positive regulation of Rac protein signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling protein localization regulation of localization cellular localization regulation of protein localization cellular component organization localization neuromuscular junction development receptor clustering cellular macromolecule localization synapse organization cellular component organization or biogenesis regulation of skeletal muscle acetylcholine-gated channel clustering regulation of receptor clustering postsynaptic membrane organization regulation of protein localization to membrane membrane organization postsynapse organization positive regulation of receptor clustering skeletal muscle acetylcholine-gated channel clustering positive regulation of protein localization to membrane localization within membrane protein localization to membrane positive regulation of skeletal muscle acetylcholine-gated channel clustering cell junction organization regulation of cellular localization macromolecule localization positive regulation of protein localization negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death protein farnesylation macromolecule modification protein prenylation metabolic process primary metabolic process protein metabolic process macromolecule metabolic process prenylation protein modification process response to peptide response to chemical response to cytokine protein geranylgeranylation regulation of biosynthetic process regulation of macromolecule metabolic process macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of nitric-oxide synthase biosynthetic process biosynthetic process positive regulation of biosynthetic process regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process positive regulation of nitric-oxide synthase biosynthetic process regulation of metabolic process nitric-oxide synthase biosynthetic process cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation negative regulation of metabolic process negative regulation of nitric-oxide synthase biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule metabolic process regulation of protein modification process positive regulation of protein deacetylation positive regulation of protein metabolic process macromolecule deacylation positive regulation of tubulin deacetylation protein deacetylation regulation of primary metabolic process positive regulation of protein modification process regulation of protein deacetylation tubulin deacetylation regulation of protein metabolic process protein deacylation regulation of tubulin deacetylation cell surface receptor signaling pathway enzyme-linked receptor protein signaling pathway response to organic cyclic compound	protein-containing complex protein farnesyltransferase complex cellular anatomical structure intracellular anatomical structure catalytic complex polyprenyl diphosphate synthase complex cytoplasm transferase complex intracellular organelle cytoskeleton organelle membraneless organelle microtubule associated complex intracellular membraneless organelle protein-containing complex protein farnesyltransferase complex cellular anatomical structure intracellular anatomical structure catalytic complex polyprenyl diphosphate synthase complex cytoplasm transferase complex intracellular organelle cytoskeleton organelle membraneless organelle microtubule associated complex intracellular membraneless organelle microtubule cytoskeleton CAAX-protein geranylgeranyltransferase complex intracellular protein-containing complex
B	Protein farnesyltransferase subunit beta	farnesyltranstransferase activity prenyltransferase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity protein farnesyltransferase activity catalytic activity, acting on a protein protein prenyltransferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding farnesyltranstransferase activity prenyltransferase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity protein farnesyltransferase activity catalytic activity, acting on a protein protein prenyltransferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process regulation of biosynthetic process regulation of macromolecule metabolic process macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process regulation of biosynthetic process regulation of macromolecule metabolic process macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of nitric-oxide synthase biosynthetic process biosynthetic process positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process positive regulation of nitric-oxide synthase biosynthetic process regulation of metabolic process nitric-oxide synthase biosynthetic process cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation fibroblast proliferation negative regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process wound healing response to stimulus response to stress response to wounding regulation of fibroblast proliferation positive regulation of fibroblast proliferation primary metabolic process lipid metabolic process response to chemical response to organic cyclic compound protein farnesylation macromolecule modification protein prenylation protein metabolic process prenylation protein modification process response to peptide response to cytokine	protein-containing complex protein farnesyltransferase complex cellular anatomical structure intracellular anatomical structure catalytic complex polyprenyl diphosphate synthase complex cytoplasm transferase complex intracellular organelle cytoskeleton organelle membraneless organelle microtubule associated complex intracellular membraneless organelle protein-containing complex protein farnesyltransferase complex cellular anatomical structure intracellular anatomical structure catalytic complex polyprenyl diphosphate synthase complex cytoplasm transferase complex intracellular organelle cytoskeleton organelle membraneless organelle microtubule associated complex intracellular membraneless organelle microtubule cytoskeleton
C	caged substrate	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002088	Protein prenyltransferase, alpha subunit	Repeat
B	IPR026872	Protein farnesyltransferase subunit beta	Family
B	IPR045089	Prenyltransferase subunit beta	Family
B	IPR008930	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Homologous Superfamily
B	IPR001330	Prenyltransferase alpha-alpha toroid domain	Domain

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.