2VNP | pdb_00002vnp

Monoclinic form of IDI-1

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)
A	d2vnpa_	Alpha and beta proteins (a+b)	Nudix	Nudix	IPP isomerase-like	Isopentenyl diphosphate isomerase	(Escherichia coli BL21 ) [TaxId: 511693 ],	SCOPe (2.08)
B	d2vnpb2	Alpha and beta proteins (a+b)	Nudix	Nudix	IPP isomerase-like	Isopentenyl diphosphate isomerase	(Escherichia coli BL21 ) [TaxId: 511693 ],	SCOPe (2.08)
B	d2vnpb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli BL21 ) [TaxId: 511693 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nudix	8033459	3000098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8033459	3000098	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		e2vnpA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
B		e2vnpB1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: CBM_14	F:	ECOD (20:10:01)

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)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00293	NUDIX domain (NUDIX)	NUDIX domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding isopentenyl-diphosphate delta-isomerase activity isomerase activity intramolecular oxidoreductase activity, transposing C=C bonds intramolecular oxidoreductase activity catalytic activity transition metal ion binding zinc ion binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular 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 cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular 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 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, B	IPR000086	NUDIX hydrolase domain	Domain
A, B	IPR056375	Isopentenyl-diphosphate delta-isomerase, bacteria	Family
A, B	IPR011876	Isopentenyl-diphosphate delta-isomerase, type 1	Family
A, B	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.