6YEH | pdb_00006yeh

Arabidopsis thaliana glutamate dehydrogenase isoform 1 in apo form

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d6yehf2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
F	d6yehf1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
E	d6yehe2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
E	d6yehe1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d6yehd2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d6yehd1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d6yehc2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d6yehc1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d6yehb2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d6yehb1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d6yeha2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d6yeha1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	MtdA-like	8095435	3000046	SCOP2B (2022-06-29)
E	SCOP2 Family	Aminoacid dehydrogenase-like	8095434	4000004	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	MtdA-like	8095435	3000046	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	MtdA-like	8095435	3000046	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MtdA-like	8095435	3000046	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MtdA-like	8095435	3000046	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MtdA-like	8095435	3000046	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	Bac_rhodopsin	e6yehF1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (develop294)
E	Bac_rhodopsin	e6yehE1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (develop294)
D	Bac_rhodopsin	e6yehD1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (develop294)
C	Bac_rhodopsin	e6yehC1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (develop294)
B	Bac_rhodopsin	e6yehB1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (develop294)
A	Bac_rhodopsin	e6yehA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (utative)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
E	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (utative)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
D	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (utative)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
C	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (utative)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
B	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (utative)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
A	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (utative)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02812	Glu/Leu/Phe/Val dehydrogenase, dimerisation domain (ELFV_dehydrog_N)	Glu/Leu/Phe/Val dehydrogenase, dimerisation domain		Domain
A, B, C, D, E A, B, C, D, E, F	PF00208	Glutamate/Leucine/Phenylalanine/Valine dehydrogenase (ELFV_dehydrog)	Glutamate/Leucine/Phenylalanine/Valine dehydrogenase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Glutamate dehydrogenase 1	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding oxidoreductase activity, acting on the CH-NH2 group of donors amino-acid dehydrogenase [NAD(P)+] activity oxidoreductase activity L-glutamate dehydrogenase [NAD(P)+] activity oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor catalytic activity adenyl ribonucleotide binding cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding oxidoreductase activity, acting on the CH-NH2 group of donors amino-acid dehydrogenase [NAD(P)+] activity oxidoreductase activity L-glutamate dehydrogenase [NAD(P)+] activity oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor catalytic activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding L-glutamate dehydrogenase (NAD+) activity copper ion binding L-glutamate dehydrogenase (NADP+) activity zinc ion binding	response to nutrient levels cellular homeostasis chemical homeostasis response to stimulus homeostatic process intracellular nitrogen homeostasis nitrogen utilization intracellular chemical homeostasis catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process dicarboxylic acid catabolic process response to nutrient levels cellular homeostasis chemical homeostasis response to stimulus homeostatic process intracellular nitrogen homeostasis nitrogen utilization intracellular chemical homeostasis catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process carboxylic acid catabolic process glutamate metabolic process small molecule metabolic process amino acid catabolic process L-glutamate catabolic process dicarboxylic acid metabolic process L-amino acid catabolic process carboxylic acid metabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process response to light stimulus response to light intensity response to radiation response to abiotic stimulus response to absence of light	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle plastid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR006095	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006096	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR006097	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, dimerisation domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014362	Glutamate dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F	IPR033524	Leu/Phe/Val dehydrogenases active site	Active Site
A, B, C, D, E A, B, C, D, E, F	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR033922	NAD(P) binding domain of glutamate dehydrogenase	Domain

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.