3DNF | pdb_00003dnf

Structure of (E)-4-Hydroxy-3-methyl-but-2-enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d3dnfa_	Alpha and beta proteins (a/b)	LytB-like	LytB-like	LytB-like	LytB	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d3dnfb_	Alpha and beta proteins (a/b)	LytB-like	LytB-like	LytB-like	LytB	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	LYTB	e3dnfA3	A: a/b three-layered sandwiches	X: HTH	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: LYTB	ECOD (v294.1)
A	LYTB	e3dnfA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase	T: NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase	F: LYTB	ECOD (v294.1)
B	RRM_1	e3dnfB2	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
B	RNA_pol_Rpb1_2	e3dnfB3	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (v294.1)
B	Hydrolase_3, HAD	e3dnfB4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Hydrolase_3, HAD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1010.20	Alpha Beta	3-Layer(aba) Sandwich	Cobalt-precorrin-4 Transmethylase	domain 1	CATH (4.3.0)
A	3.40.50.11270	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.1010.20	Alpha Beta	3-Layer(aba) Sandwich	Cobalt-precorrin-4 Transmethylase	domain 1	CATH (4.3.0)
B	3.40.50.11270	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02401	LytB protein (LYTB)	LytB protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid biosynthetic process aldehyde metabolic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid biosynthetic process aldehyde metabolic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process isoprenoid metabolic process isopentenyl diphosphate metabolic process terpenoid biosynthetic process terpenoid metabolic process dimethylallyl diphosphate biosynthetic process dimethylallyl diphosphate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003451	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	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.

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