3JD4 | pdb_00003jd4

Glutamate dehydrogenase in complex with NADH and GTP, closed conformation

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)
A	SCOP2B Superfamily	MtdA-like	8054255	3000046	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	MtdA-like	8054255	3000046	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	MtdA-like	8054255	3000046	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MtdA-like	8054255	3000046	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MtdA-like	8054255	3000046	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MtdA-like	8054255	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)
A		e3jd4A2	A: Ribosomal protein L31e-like	X: Ribosomal protein L31e/gp120 outer domain	H: Ribosomal protein L31e/gp120 outer domain	T: Glyco_transf_41	F:	ECOD (20:10:01)
A		e3jd4A3	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: HAT_PRP39_N, HAT_PRP39_C	F:	ECOD (20:10:01)
F		e3jd4F2	A: Ribosomal protein L31e-like	X: Ribosomal protein L31e/gp120 outer domain	H: Ribosomal protein L31e/gp120 outer domain	T: Glyco_transf_41	F:	ECOD (20:10:01)
F		e3jd4F3	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: HAT_PRP39_N, HAT_PRP39_C	F:	ECOD (20:10:01)
E		e3jd4E2	A: Ribosomal protein L31e-like	X: Ribosomal protein L31e/gp120 outer domain	H: Ribosomal protein L31e/gp120 outer domain	T: Glyco_transf_41	F:	ECOD (20:10:01)
E		e3jd4E3	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: HAT_PRP39_N, HAT_PRP39_C	F:	ECOD (20:10:01)
D		e3jd4D2	A: Ribosomal protein L31e-like	X: Ribosomal protein L31e/gp120 outer domain	H: Ribosomal protein L31e/gp120 outer domain	T: Glyco_transf_41	F:	ECOD (20:10:01)
D		e3jd4D3	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: HAT_PRP39_N, HAT_PRP39_C	F:	ECOD (20:10:01)
C		e3jd4C1	A: Ribosomal protein L31e-like	X: Ribosomal protein L31e/gp120 outer domain	H: Ribosomal protein L31e/gp120 outer domain	T: Glyco_transf_41	F:	ECOD (20:10:01)
C		e3jd4C2	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: HAT_PRP39_N, HAT_PRP39_C	F:	ECOD (20:10:01)
B		e3jd4B1	A: Ribosomal protein L31e-like	X: Ribosomal protein L31e/gp120 outer domain	H: Ribosomal protein L31e/gp120 outer domain	T: Glyco_transf_41	F:	ECOD (20:10:01)
B		e3jd4B2	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: HAT_PRP39_N, HAT_PRP39_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.287.140	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
A	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	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)
F	1.10.287.140	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
F	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	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)
E	1.10.287.140	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
E	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	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)
D	1.10.287.140	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	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)
C	1.10.287.140	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
C	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	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)
B	1.10.287.140	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	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)

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, mitochondrial	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 binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding L-glutamate dehydrogenase (NAD+) activity L-glutamate dehydrogenase (NADP+) activity guanyl nucleotide binding GTP binding guanyl ribonucleotide binding identical protein binding protein binding	tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process catabolic process amino acid metabolic process organic acid catabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process carboxylic acid catabolic process glutamate metabolic process tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process catabolic process amino acid metabolic process organic acid catabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process carboxylic acid catabolic process glutamate metabolic process amino acid catabolic process L-glutamate catabolic process dicarboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process glutamine metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane endoplasmic reticulum endomembrane system

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	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.