5XK3 | pdb_00005xk3

Crystal structure of apo form Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp. strain CNH-189

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D	d5xk3d1	Alpha and beta proteins (a/b)	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	automated matches	automated matches	(Streptomyces sp. CNH189 ) [TaxId: 1136432 ],	SCOPe (2.08)
D	d5xk3d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptomyces sp. CNH189 ) [TaxId: 1136432 ],	SCOPe (2.08)
C	d5xk3c_	Alpha and beta proteins (a/b)	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	automated matches	automated matches	(Streptomyces sp. CNH189 ) [TaxId: 1136432 ],	SCOPe (2.08)
B	d5xk3b1	Alpha and beta proteins (a/b)	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	automated matches	automated matches	(Streptomyces sp. CNH189 ) [TaxId: 1136432 ],	SCOPe (2.08)
B	d5xk3b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptomyces sp. CNH189 ) [TaxId: 1136432 ],	SCOPe (2.08)
A	d5xk3a1	Alpha and beta proteins (a/b)	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	automated matches	automated matches	(Streptomyces sp. CNH189 ) [TaxId: 1136432 ],	SCOPe (2.08)
A	d5xk3a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptomyces sp. CNH189 ) [TaxId: 1136432 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Undecaprenyl diphosphate synthase	8067728	3000594	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Undecaprenyl diphosphate synthase	8067728	3000594	SCOP2B (2022-06-29)
B	SCOP2 Family	Undecaprenyl diphosphate synthase-like	8067727	4003318	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Undecaprenyl diphosphate synthase	8067728	3000594	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Undecaprenyl diphosphate synthase	8067728	3000594	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	ATP-synt_VA_C	e5xk3D1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_VA_C	ECOD (v294.1)
C	ATP-synt_VA_C	e5xk3C1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_VA_C	ECOD (v294.1)
B	ATP-synt_VA_C	e5xk3B1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_VA_C	ECOD (v294.1)
A	ATP-synt_VA_C	e5xk3A1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_VA_C	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Undecaprenyl diphosphate synthase	prenyl diphosphate synthase activity prenyltransferase activity ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity cation binding ion binding binding metal ion binding small molecule binding	polyprenol metabolic process polyprenol biosynthetic process small molecule biosynthetic process isoprenoid biosynthetic process lipid biosynthetic process alcohol metabolic process primary metabolic process biosynthetic process alcohol biosynthetic process small molecule metabolic process metabolic process cellular process isoprenoid metabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036424	Decaprenyl diphosphate synthase-like superfamily	Homologous Superfamily
A, B, C, D	IPR001441	Decaprenyl diphosphate synthase-like	Family

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.