7Q56 | pdb_00007q56

Single Particle Cryo-EM structure of photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
P [auth F]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
N [auth H]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
L [auth P]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
J [auth R]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
H [auth D]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
D [auth L]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
B [auth J]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
O [auth E]	SCOP2B Superfamily	GAPDH-like	8068923	3000043	SCOP2B (2022-06-29)
M [auth G]	SCOP2B Superfamily	GAPDH-like	8068923	3000043	SCOP2B (2022-06-29)
K [auth O]	SCOP2B Superfamily	GAPDH-like	8068923	3000043	SCOP2B (2022-06-29)
I [auth Q]	SCOP2B Superfamily	GAPDH-like	8068923	3000043	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	GAPDH-like	8068923	3000043	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	GAPDH-like	8068923	3000043	SCOP2B (2022-06-29)
C [auth K]	SCOP2B Superfamily	GAPDH-like	8068923	3000043	SCOP2B (2022-06-29)
A [auth I]	SCOP2B Superfamily	GAPDH-like	8068923	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)
P [auth F]	Gp_dh_C	e7q56F2	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)
P [auth F]	Gp_dh_N	e7q56F1	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)
N [auth H]	Gp_dh_C	e7q56H1	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)
N [auth H]	Gp_dh_N	e7q56H2	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)
L [auth P]	Gp_dh_C	e7q56P1	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)
L [auth P]	Gp_dh_N	e7q56P2	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)
J [auth R]	Gp_dh_C	e7q56R2	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)
J [auth R]	Gp_dh_N	e7q56R1	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)
H [auth D]	Gp_dh_C	e7q56D1	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)
H [auth D]	Gp_dh_N	e7q56D2	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)
F [auth B]	Gp_dh_C	e7q56B2	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 B]	Gp_dh_N	e7q56B1	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)
D [auth L]	Gp_dh_C	e7q56L2	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)
D [auth L]	Gp_dh_N	e7q56L1	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 [auth J]	Gp_dh_C	e7q56J1	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 [auth J]	Gp_dh_N	e7q56J2	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)
O [auth E]	Gp_dh_C	e7q56E2	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)
O [auth E]	Gp_dh_N	e7q56E1	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)
M [auth G]	Gp_dh_C	e7q56G1	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)
M [auth G]	Gp_dh_N	e7q56G2	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)
K [auth O]	Gp_dh_C	e7q56O2	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)
K [auth O]	Gp_dh_N	e7q56O1	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)
I [auth Q]	Gp_dh_C	e7q56Q2	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)
I [auth Q]	Gp_dh_N	e7q56Q1	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)
G [auth C]	Gp_dh_C	e7q56C1	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)
G [auth C]	Gp_dh_N	e7q56C2	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 A]	Gp_dh_C	e7q56A1	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 A]	Gp_dh_N	e7q56A2	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)
C [auth K]	Gp_dh_C	e7q56K2	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)
C [auth K]	Gp_dh_N	e7q56K1	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 [auth I]	Gp_dh_C	e7q56I2	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 [auth I]	Gp_dh_N	e7q56I1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth J], D [auth L], F [auth B], H [auth D], J [auth R], B [auth J], D [auth L], F [auth B], H [auth D], J [auth R], L [auth P], N [auth H], P [auth F]	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
B [auth J], D [auth L], F [auth B], H [auth D], J [auth R], B [auth J], D [auth L], F [auth B], H [auth D], J [auth R], L [auth P], N [auth H], P [auth F]	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
A [auth I], C [auth K], E [auth A], G [auth C], I [auth Q], A [auth I], C [auth K], E [auth A], G [auth C], I [auth Q], K [auth O], M [auth G], O [auth E]	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 I], C [auth K], E [auth A], G [auth C], I [auth Q], A [auth I], C [auth K], E [auth A], G [auth C], I [auth Q], K [auth O], M [auth G], O [auth E]	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
B [auth J], D [auth L], F [auth B], H [auth D], J [auth R], B [auth J], D [auth L], F [auth B], H [auth D], J [auth R], L [auth P], N [auth H], P [auth F]	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic	binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) 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 binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) 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 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity NAD binding	carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process carbon fixation monosaccharide metabolic process hexose metabolic process small molecule metabolic process glucose metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast
A [auth I], C [auth K], E [auth A], G [auth C], I [auth Q], A [auth I], C [auth K], E [auth A], G [auth C], I [auth Q], K [auth O], M [auth G], O [auth E]	Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic	binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) 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 binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) 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 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity NAD binding	carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process carbon fixation monosaccharide metabolic process hexose metabolic process small molecule metabolic process glucose metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

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

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 7Q56 | pdb_00007q56

Single Particle Cryo-EM structure of photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea.

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

7Q56 | pdb_00007q56