6G31 | pdb_00006g31

Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y bound to zoledronate

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)
L	d6g31l_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d6g31k_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d6g31j_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d6g31i_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d6g31h_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6g31g_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6g31f_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6g31e_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6g31d_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6g31c_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6g31b_	All alpha proteins	Terpenoid synthases	Terpenoid synthases	Isoprenyl diphosphate synthases	Geranylgeranyl pyrophosphate synthetase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6g31a_	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)
L	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Terpenoid synthases	8035279	3001615	SCOP2B (2022-06-29)
A	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)
L	polyprenyl_synt	e6g31L1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)
K	polyprenyl_synt	e6g31K1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)
J	polyprenyl_synt	e6g31J1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)
I	polyprenyl_synt	e6g31I1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)
H	polyprenyl_synt	e6g31H1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)
G	polyprenyl_synt	e6g31G1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)
F	polyprenyl_synt	e6g31F1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)
E	polyprenyl_synt	e6g31E1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)
D	polyprenyl_synt	e6g31D1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)
C	polyprenyl_synt	e6g31C1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)
B	polyprenyl_synt	e6g31B1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)
A	polyprenyl_synt	e6g31A1	A: alpha bundles	X: Terpenoid synthases (From Topology)	H: Terpenoid synthases (From Topology)	T: Terpenoid synthases	F: polyprenyl_synt	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)
K	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)
J	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)
I	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)
H	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)
G	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)
F	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)
E	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)
D	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)
C	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)
B	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)
A	1.10.600.10	Mainly Alpha	Orthogonal Bundle	Farnesyl Diphosphate Synthase	Farnesyl Diphosphate Synthase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR008949	Isoprenoid synthase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR033749	Polyprenyl synthetase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR000092	Polyprenyl synthetase-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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.