3RVD | pdb_00003rvd

Crystal structure of the binary complex, obtained by soaking, of photosyntetic a4 glyceraldehyde 3-phosphate dehydrogenase (gapdh) with cp12-2, both from arabidopsis thaliana.

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)
P [auth Q]	SCOP2B Superfamily	GAPDH-like	8068927	3000043	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	GAPDH-like	8068927	3000043	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	GAPDH-like	8068927	3000043	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	GAPDH-like	8068927	3000043	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GAPDH-like	8068927	3000043	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GAPDH-like	8068927	3000043	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GAPDH-like	8068927	3000043	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GAPDH-like	8068927	3000043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8068927	3000043	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GAPDH-like	8068927	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 Q]	Gp_dh_C	e3rvdQ1	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 Q]	Gp_dh_N	e3rvdQ2	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	Gp_dh_C	e3rvdO1	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	Gp_dh_N	e3rvdO2	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	Gp_dh_C	e3rvdH1	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	Gp_dh_N	e3rvdH2	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	Gp_dh_C	e3rvdG1	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	Gp_dh_N	e3rvdG2	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	Gp_dh_C	e3rvdF1	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	Gp_dh_N	e3rvdF2	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	Gp_dh_C	e3rvdE1	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	Gp_dh_N	e3rvdE2	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	Gp_dh_C	e3rvdD1	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	Gp_dh_N	e3rvdD2	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	Gp_dh_C	e3rvdC1	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	Gp_dh_N	e3rvdC2	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	e3rvdB1	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	e3rvdB2	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	e3rvdA1	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	e3rvdA2	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)
P [auth Q]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
P [auth Q]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
O	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
O	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	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, C, D, E, A, B, C, D, E, F, G, H, O, P [auth Q]	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, D, E, A, B, C, D, E, F, G, H, O, P [auth Q]	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
I, J, K, L, M I, J, K, L, M, N	Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding protein-containing complex binding copper ion binding protein binding enzyme binding protein-macromolecule adaptor activity molecular adaptor activity	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process carbon fixation cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus cellular response to cold response to cold response to light stimulus response to radiation peptide cross-linking via L-cystine peptidyl-cysteine modification macromolecule modification peptide cross-linking peptidyl-amino acid modification protein metabolic process macromolecule metabolic process protein modification process response to decreased oxygen levels cellular response to oxygen levels cellular response to decreased oxygen levels cellular response to anoxia cellular response to chemical stimulus response to anoxia response to chemical response to oxygen levels regulation of cellular process negative regulation of biological process 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 regulation of biological process regulation of photosynthesis negative regulation of metabolic process biological regulation negative regulation of biosynthetic process negative regulation of photosynthesis regulation of carbohydrate biosynthetic process regulation of metabolic process negative regulation of reductive pentose-phosphate cycle response to carbohydrate response to sucrose response to disaccharide response to oxygen-containing compound	membrane-bounded organelle intracellular anatomical structure plastid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure plastid stroma organelle chloroplast stroma cytoplasm chloroplast cytosol protein-containing complex supramolecular complex
A, B, C, D, E, A, B, C, D, E, F, G, H, O, P [auth Q]	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic	salicylic acid binding organic acid binding binding ion binding anion binding carboxylic acid binding monocarboxylic acid binding small molecule binding RNA binding nucleic acid binding mRNA binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding salicylic acid binding organic acid binding binding ion binding anion binding carboxylic acid binding monocarboxylic acid binding small molecule binding RNA binding nucleic acid binding mRNA binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding identical protein binding protein binding protein homodimerization activity protein dimerization activity 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 disordered domain specific binding protein domain specific binding	response to stimulus response to stress response to abiotic stimulus response to cold response to temperature stimulus carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process response to stimulus response to stress response to abiotic stimulus response to cold response to temperature stimulus 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 protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis response to light stimulus response to radiation response to carbohydrate response to sucrose response to disaccharide response to chemical response to oxygen-containing compound monosaccharide metabolic process hexose metabolic process small molecule metabolic process glucose metabolic process	membrane-bounded organelle intracellular anatomical structure plastid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure plastid stroma organelle chloroplast stroma cytoplasm chloroplast cytosol extracellular region apoplast membrane-bounded organelle intracellular anatomical structure plastid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure plastid stroma organelle chloroplast stroma cytoplasm chloroplast cytosol extracellular region apoplast supramolecular complex chloroplast thylakoid membrane plastid membrane organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle membraneless organelle plastid envelope thylakoid membrane intracellular membraneless organelle thylakoid membrane chloroplast thylakoid outer membrane photosynthetic membrane organelle membrane chloroplast envelope chloroplast membrane stromule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I, J, K, L, M I, J, K, L, M, N	IPR003823	CP12 domain	Domain
I, J, K, L, M I, J, K, L, M, N	IPR039314	Calvin cycle protein CP12-like	Family
A, B, C, D, E, A, B, C, D, E, F, G, H, O, P [auth Q]	IPR020830	Glyceraldehyde 3-phosphate dehydrogenase, active site	Active Site
A, B, C, D, E, A, B, C, D, E, F, G, H, O, P [auth Q]	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family	Family
A, B, C, D, E, A, B, C, D, E, F, G, H, O, P [auth Q]	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, O, P [auth Q]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, O, P [auth Q]	IPR020829	Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, O, P [auth Q]	IPR006424	Glyceraldehyde-3-phosphate dehydrogenase, type I	Family