3WYJ | pdb_00003wyj

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789

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)
B	d3wyjb_	Alpha and beta proteins (a/b)	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3wyja_	Alpha and beta proteins (a/b)	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	Undecaprenyl diphosphate synthase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Undecaprenyl diphosphate synthase	8033493	3000594	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Undecaprenyl diphosphate synthase	8033493	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)
B	Chlor_dismutase	e3wyjB1	A: alpha bundles	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Chlor_dismutase	ECOD (develop294)
A	Beta-Casp	e3wyjA1	A: alpha bundles	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.1180.10	Alpha Beta	3-Layer(aba) Sandwich	Undecaprenyl pyrophosphate synthetase	Decaprenyl diphosphate synthase-like	CATH (4.3.0)
A	3.40.1180.10	Alpha Beta	3-Layer(aba) Sandwich	Undecaprenyl pyrophosphate synthetase	Decaprenyl diphosphate synthase-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01255	Putative undecaprenyl diphosphate synthase (Prenyltransf)	Putative undecaprenyl diphosphate synthase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity prenyl diphosphate synthase activity ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity prenyltransferase activity ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity prenyl diphosphate synthase activity ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] 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	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular component biogenesis peptidoglycan-based cell wall biogenesis Gram-negative-bacterium-type cell wall biogenesis developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular component biogenesis peptidoglycan-based cell wall biogenesis Gram-negative-bacterium-type cell wall biogenesis cell wall biogenesis cell wall organization or biogenesis cellular process cellular component organization or biogenesis cell division cellular component organization cell wall organization external encapsulating structure organization 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 isoprenoid metabolic process lipid metabolic process carbohydrate derivative biosynthetic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process peptidoglycan biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process glycosaminoglycan biosynthetic process macromolecule metabolic process cell wall macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001441	Decaprenyl diphosphate synthase-like	Family
A, B	IPR018520	Di-trans-poly-cis-decaprenylcistransferase-like, conserved site	Conserved Site
A, B	IPR036424	Decaprenyl diphosphate synthase-like superfamily	Homologous Superfamily

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.