3E6A | pdb_00003e6a

Crystal structure and Functional Analysis of Glyceraldehyde-3-phosphate Dehydrogenase from Oryza Sativa

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth C]	SCOP2B Superfamily	GAPDH-like	8068863	3000043	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	GAPDH-like	8068863	3000043	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	GAPDH-like	8068863	3000043	SCOP2B (2022-06-29)
A [auth O]	SCOP2B Superfamily	GAPDH-like	8068863	3000043	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)
D [auth C]	YgbB	e3e6aC1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (develop294)
C [auth B]	YgbB	e3e6aB1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (develop294)
B [auth A]	YgbB	e3e6aA1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (develop294)
A [auth O]	YgbB	e3e6aO1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth C]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D [auth C]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
C [auth B]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C [auth B]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
B [auth A]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B [auth A]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
A [auth O]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A [auth O]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth O], B [auth A], C [auth B], D [auth C]	PF02800	Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain (Gp_dh_C)	Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain	GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold.	Domain
A [auth O], B [auth A], C [auth B], D [auth C]	PF00044	Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain (Gp_dh_N)	Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain	GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth O], B [auth A], C [auth B], D [auth C]	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic	NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding phosphate ion binding NADP binding glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding phosphate ion binding NADP binding glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration catabolic process ATP metabolic process energy derivation by oxidation of organic compounds purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process cellular process purine ribonucleoside diphosphate catabolic process monosaccharide metabolic process hexose metabolic process glucose metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth O], B [auth A], C [auth B], D [auth C]	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain	Domain
A [auth O], B [auth A], C [auth B], D [auth C]	IPR020830	Glyceraldehyde 3-phosphate dehydrogenase, active site	Active Site
A [auth O], B [auth A], C [auth B], D [auth C]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A [auth O], B [auth A], C [auth B], D [auth C]	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family	Family
A [auth O], B [auth A], C [auth B], D [auth C]	IPR020829	Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain	Domain
A [auth O], B [auth A], C [auth B], D [auth C]	IPR006424	Glyceraldehyde-3-phosphate dehydrogenase, type I	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.