3B1K | pdb_00003b1k

Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with CP12 in the absence of copper from Synechococcus elongatus

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)
F [auth H]	SCOP2B Superfamily	GAPDH-like	8068917	3000043	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	GAPDH-like	8068917	3000043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8068917	3000043	SCOP2B (2022-06-29)
A	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)
F [auth H]	Gp_dh_C	e3b1kH1	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: Gp_dh_C	ECOD (1.6)
F [auth H]	Gp_dh_N	e3b1kH2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Gp_dh_N	ECOD (1.6)
E [auth G]	Gp_dh_C	e3b1kG1	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: Gp_dh_C	ECOD (1.6)
E [auth G]	Gp_dh_N	e3b1kG2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Gp_dh_N	ECOD (1.6)
B	Gp_dh_C	e3b1kB1	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: Gp_dh_C	ECOD (1.6)
B	Gp_dh_N	e3b1kB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Gp_dh_N	ECOD (1.6)
A	Gp_dh_C	e3b1kA1	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: Gp_dh_C	ECOD (1.6)
A	Gp_dh_N	e3b1kA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Gp_dh_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth H]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F [auth H]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
E [auth G]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E [auth G]	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E [auth G], F [auth H]	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, E [auth G], F [auth H]	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
C, D, G [auth I], H [auth J]	CP12	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	regulation of cellular process photosynthesis negative regulation of biological process photosynthesis, dark reaction regulation of photosynthesis, dark reaction regulation of reductive pentose-phosphate cycle regulation of primary metabolic process negative regulation of cellular process regulation of carbohydrate metabolic process negative regulation of carbohydrate metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process regulation of photosynthesis regulation of cellular process photosynthesis negative regulation of biological process photosynthesis, dark reaction regulation of photosynthesis, dark reaction regulation of reductive pentose-phosphate cycle regulation of primary metabolic process negative regulation of cellular process regulation of carbohydrate metabolic process negative regulation of carbohydrate metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process regulation of photosynthesis negative regulation of metabolic process carbohydrate biosynthetic process biological regulation primary metabolic process biosynthetic process negative regulation of biosynthetic process reductive pentose-phosphate cycle cellular process metabolic process negative regulation of photosynthesis regulation of carbohydrate biosynthetic process regulation of metabolic process negative regulation of reductive pentose-phosphate cycle carbon fixation	-
A, B, E [auth G], F [auth H]	Glyceraldehyde 3-phosphate dehydrogenase (NADP+)	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 adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding NAD binding cation 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 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 hexose metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process glucose metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D, G [auth I], H [auth J]	IPR039314	Calvin cycle protein CP12-like	Family
C, D, G [auth I], H [auth J]	IPR003823	CP12 domain	Domain
A, B, E [auth G], F [auth H]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, E [auth G], F [auth H]	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family	Family
A, B, E [auth G], F [auth H]	IPR020829	Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain	Domain
A, B, E [auth G], F [auth H]	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain	Domain
A, B, E [auth G], F [auth H]	IPR020830	Glyceraldehyde 3-phosphate dehydrogenase, active site	Active Site
A, B, E [auth G], F [auth H]	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.