1YJ8 | pdb_00001yj8

Initial structural analysis of Plasmodium falciparum Glycerol-3-phosphate dehydrogenase

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)
C	d1yj8c2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
C	d1yj8c1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
B	d1yj8b2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
B	d1yj8b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
A	d1yj8a2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
A	d1yj8a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Ank_2, Ank_4, Ank_5	e1yj8C3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (develop294)
B	Ank_2, Ank_4, Ank_5	e1yj8B3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (develop294)
A	Ank_2, Ank_4, Ank_5	e1yj8A3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF07479	NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus (NAD_Gly3P_dh_C)	NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus	NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyses the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the C-terminal substrate-binding domain [2].	Domain
A, B, C	PF01210	NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus (NAD_Gly3P_dh_N)	NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	glycerol-3-phosphate dehydrogenase	glycerol-3-phosphate dehydrogenase [NAD(P)+] activity oxidoreductase activity glycerol-3-phosphate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity NAD binding nucleoside phosphate binding purine nucleotide binding glycerol-3-phosphate dehydrogenase [NAD(P)+] activity oxidoreductase activity glycerol-3-phosphate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity NAD binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding	carbohydrate derivative catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process glycerol-3-phosphate catabolic process glycerol-3-phosphate metabolic process organophosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process alditol phosphate metabolic process phosphorus metabolic process carbohydrate metabolic process primary metabolic process	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex oxidoreductase complex cytoplasm glycerol-3-phosphate dehydrogenase (FAD) complex cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR017751	Glycerol-3-phosphate dehydrogenase, NAD-dependent, eukaryotic	Family
A, B, C	IPR006109	Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal	Domain
A, B, C	IPR011128	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal	Domain
A, B, C	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C	IPR013328	6-phosphogluconate dehydrogenase, domain 2	Homologous Superfamily
A, B, C	IPR006168	Glycerol-3-phosphate dehydrogenase, NAD-dependent	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.