3HYQ | pdb_00003hyq

Crystal Structure of Isopentenyl-Diphosphate delta-Isomerase from Salmonella entericase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d3hyqa_	Alpha and beta proteins (a+b)	Nudix	Nudix	IPP isomerase-like	Isopentenyl diphosphate isomerase	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	IPP isomerase-like	8085442	4003621	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nudix	8085443	3000098	SCOP2 (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	Pep_deformylase	e3hyqA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: FAD-dependent thiol oxidase	T: FAD-dependent thiol oxidase	F: Pep_deformylase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Isopentenyl-diphosphate Delta-isomerase	isopentenyl-diphosphate delta-isomerase activity isomerase activity intramolecular oxidoreductase activity, transposing C=C bonds intramolecular oxidoreductase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	lipid biosynthetic process primary metabolic process phospholipid biosynthetic process phospholipid metabolic process dimethylallyl diphosphate biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process dimethylallyl diphosphate metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process lipid biosynthetic process primary metabolic process phospholipid biosynthetic process phospholipid metabolic process dimethylallyl diphosphate biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process dimethylallyl diphosphate metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process isoprenoid biosynthetic process isoprenoid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000086	NUDIX hydrolase domain	Domain
A	IPR056375	Isopentenyl-diphosphate delta-isomerase, bacteria	Family
A	IPR011876	Isopentenyl-diphosphate delta-isomerase, type 1	Family
A	IPR015797	NUDIX hydrolase-like domain 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.