6R4V | pdb_00006r4v

Crystal structure of human geranylgeranyl diphosphate synthase bound to ibandronate

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6r4va_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d6r4vc_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth F]	d6r4vf_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth E]	d6r4ve_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d6r4vb_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth D]	d6r4vd_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	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	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	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	Metallophos	e6r4vA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Metallophos	ECOD (v294.1)
B [auth C]	MAM33	e6r4vC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: MAM33	ECOD (v294.1)
C [auth F]	Metallophos	e6r4vF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Metallophos	ECOD (v294.1)
D [auth E]	Metallophos	e6r4vE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Metallophos	ECOD (v294.1)
E [auth B]	Metallophos	e6r4vB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Metallophos	ECOD (v294.1)
F [auth D]	Metallophos	e6r4vD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Metallophos	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (utative)
B [auth C]	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (utative)
C [auth F]	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (utative)
D [auth E]	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (utative)
E [auth B]	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (utative)
F [auth D]	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth F], D [auth E], E [auth B], A, B [auth C], C [auth F], D [auth E], E [auth B], F [auth D]	PF00348	Polyprenyl synthetase (polyprenyl_synt)	Polyprenyl synthetase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth F], D [auth E], E [auth B], A, B [auth C], C [auth F], D [auth E], E [auth B], F [auth D]	Geranylgeranyl pyrophosphate synthase	prenyl diphosphate synthase activity dimethylallyltranstransferase activity prenyltransferase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity geranylgeranyl diphosphate synthase activity (2E,6E)-farnesyl diphosphate synthase activity cation binding ion binding binding metal ion binding small molecule binding identical protein binding prenyl diphosphate synthase activity dimethylallyltranstransferase activity prenyltransferase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity geranylgeranyl diphosphate synthase activity (2E,6E)-farnesyl diphosphate synthase activity cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	primary metabolic process metabolic process cellular process isoprenoid metabolic process lipid metabolic process isoprenoid biosynthetic process lipid biosynthetic process terpenoid biosynthetic process phospholipid biosynthetic process farnesyl diphosphate metabolic process phospholipid metabolic process biosynthetic process farnesyl diphosphate biosynthetic process organophosphate metabolic process primary metabolic process metabolic process cellular process isoprenoid metabolic process lipid metabolic process isoprenoid biosynthetic process lipid biosynthetic process terpenoid biosynthetic process phospholipid biosynthetic process farnesyl diphosphate metabolic process phospholipid metabolic process biosynthetic process farnesyl diphosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process terpenoid metabolic process geranyl diphosphate biosynthetic process geranyl diphosphate metabolic process geranylgeranyl diphosphate biosynthetic process geranylgeranyl diphosphate metabolic process	intracellular anatomical structure intracellular membraneless organelle Z disc sarcomere intracellular organelle I band cellular anatomical structure organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer intracellular anatomical structure intracellular membraneless organelle Z disc sarcomere intracellular organelle I band cellular anatomical structure organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex cytosol perinuclear region of cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth F], D [auth E], E [auth B], A, B [auth C], C [auth F], D [auth E], E [auth B], F [auth D]	IPR008949	Isoprenoid synthase domain superfamily	Homologous Superfamily
A, B [auth C], C [auth F], D [auth E], E [auth B], A, B [auth C], C [auth F], D [auth E], E [auth B], F [auth D]	IPR033749	Polyprenyl synthetase, conserved site	Conserved Site
A, B [auth C], C [auth F], D [auth E], E [auth B], A, B [auth C], C [auth F], D [auth E], E [auth B], F [auth D]	IPR000092	Polyprenyl synthetase-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth C], C [auth F], D [auth E], E [auth B], A, B [auth C], C [auth F], D [auth E], E [auth B], F [auth D]	Pharos: O95749	breast cancer gastric carcinoma ovarian cancer psoriasis congenital muscular dystrophy hepatocellular carcinoma pancreatic intraductal papillary-mucinous carcinoma tuberculosis gastric cancer malignant ependymoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.