Annotations: 7Q55

Single Particle Cryo-EM structure of photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase hexadecamer (major conformer) from Spinacia oleracia.

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 L]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
N [auth J]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
L [auth H]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
J [auth F]	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 R]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
B [auth P]	SCOP2B Superfamily	GAPDH-like	8056136	3000043	SCOP2B (2022-06-29)
O [auth K]	SCOP2B Superfamily	GAPDH-like	8068923	3000043	SCOP2B (2022-06-29)
M [auth I]	SCOP2B Superfamily	GAPDH-like	8068923	3000043	SCOP2B (2022-06-29)
K [auth G]	SCOP2B Superfamily	GAPDH-like	8068923	3000043	SCOP2B (2022-06-29)
I [auth E]	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 Q]	SCOP2B Superfamily	GAPDH-like	8068923	3000043	SCOP2B (2022-06-29)
A [auth O]	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 L]	tRNA-synt_2	e7q55L1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
N [auth J]	tRNA-synt_2	e7q55J1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
L [auth H]	tRNA-synt_2	e7q55H1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
J [auth F]	tRNA-synt_2	e7q55F1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
H [auth D]	tRNA-synt_2	e7q55D1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
F [auth B]	tRNA-synt_2	e7q55B1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
D [auth R]	tRNA-synt_2	e7q55R1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
B [auth P]	tRNA-synt_2	e7q55P1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
O [auth K]	tRNA-synt_2	e7q55K1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
M [auth I]	tRNA-synt_2	e7q55I1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
K [auth G]	tRNA-synt_2	e7q55G1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
I [auth E]	tRNA-synt_2	e7q55E1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
G [auth C]	tRNA-synt_2	e7q55C1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
E [auth A]	tRNA-synt_2	e7q55A1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
C [auth Q]	tRNA-synt_2	e7q55Q1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)
A [auth O]	tRNA-synt_2	e7q55O1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

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

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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.