2DUU

Crystal Structure of apo-form of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp.

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)
A	SCOP2 Family	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like	8068916	4000077	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAPDH-like	8068917	3000043	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8068917	3000043	SCOP2B (2022-06-29)
C [auth O]	SCOP2B Superfamily	GAPDH-like	8068917	3000043	SCOP2B (2022-06-29)
E [auth Q]	SCOP2B Superfamily	GAPDH-like	8068917	3000043	SCOP2B (2022-06-29)
D [auth P]	SCOP2B Superfamily	GAPDH-like	8068917	3000043	SCOP2B (2022-06-29)
F [auth R]	SCOP2B Superfamily	GAPDH-like	8068917	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)
A	PF02800	e2duuA1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: PF02800	ECOD (1.6)
A	PF00044	e2duuA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF00044	ECOD (1.6)
B	PF02800	e2duuB1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: PF02800	ECOD (1.6)
B	PF00044	e2duuB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF00044	ECOD (1.6)
C [auth O]	PF02800	e2duuO1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: PF02800	ECOD (1.6)
C [auth O]	PF00044	e2duuO2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF00044	ECOD (1.6)
E [auth Q]	PF02800	e2duuQ1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: PF02800	ECOD (1.6)
E [auth Q]	PF00044	e2duuQ2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF00044	ECOD (1.6)
D [auth P]	PF02800	e2duuP1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: PF02800	ECOD (1.6)
D [auth P]	PF00044	e2duuP2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF00044	ECOD (1.6)
F [auth R]	PF02800	e2duuR1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: PF02800	ECOD (1.6)
F [auth R]	PF00044	e2duuR2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF00044	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	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	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
C [auth O]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C [auth O]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
E [auth Q]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E [auth Q]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
D [auth P]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D [auth P]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
F [auth R]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F [auth R]	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, B, C [auth O], D [auth P], E [auth Q], A, B, C [auth O], D [auth P], E [auth Q], F [auth R]	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, B, C [auth O], D [auth P], E [auth Q], A, B, C [auth O], D [auth P], E [auth Q], F [auth R]	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, B, C [auth O], D [auth P], E [auth Q], A, B, C [auth O], D [auth P], E [auth Q], F [auth R]	Glyceraldehyde 3-phosphate dehydrogenase	oxidoreductase 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 binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding NAD binding oxidoreductase 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 binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding NAD binding cation binding ion binding metal ion binding	monosaccharide metabolic process carbohydrate metabolic process organic substance metabolic process hexose metabolic process small molecule metabolic process metabolic process primary metabolic process glucose metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.