5IJZ | pdb_00005ijz

Crystal structure of glutamate dehydrogenase(GDH) from Corynebacterium glutamicum

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)
L	d5ijzl2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
L	d5ijzl1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
K	d5ijzk2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
K	d5ijzk1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
J	d5ijzj2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
J	d5ijzj1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
I	d5ijzi2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
I	d5ijzi1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
H	d5ijzh2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
H	d5ijzh1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
G	d5ijzg2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
G	d5ijzg1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
F	d5ijzf2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
F	d5ijzf1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
E	d5ijze2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
E	d5ijze1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
D	d5ijzd2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
D	d5ijzd1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
C	d5ijzc2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
C	d5ijzc1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
B	d5ijzb2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
B	d5ijzb1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
A	d5ijza2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)
A	d5ijza1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ATCC 13032 ) [TaxId: 196627 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	MtdA-like	8067029	3000046	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	MtdA-like	8067029	3000046	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	MtdA-like	8067029	3000046	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	MtdA-like	8067029	3000046	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	MtdA-like	8067029	3000046	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	MtdA-like	8067029	3000046	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	MtdA-like	8067029	3000046	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MtdA-like	8067029	3000046	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MtdA-like	8067029	3000046	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MtdA-like	8067029	3000046	SCOP2B (2022-06-29)
A	SCOP2 Family	Aminoacid dehydrogenase-like	8067028	4000004	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MtdA-like	8067029	3000046	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L		e5ijzL1	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F:	ECOD (v294.1)
L	HTH_65	e5ijzL2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: HTH_65	ECOD (v294.1)
K	Usher	e5ijzK2	A: a/b three-layered sandwiches	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: Usher	ECOD (v294.1)
J		e5ijzJ1	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F:	ECOD (v294.1)
J	HTH_65	e5ijzJ2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: HTH_65	ECOD (v294.1)
I		e5ijzI1	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F:	ECOD (v294.1)
I	HTH_65	e5ijzI2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: HTH_65	ECOD (v294.1)
H		e5ijzH1	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F:	ECOD (v294.1)
H	HTH_65	e5ijzH2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: HTH_65	ECOD (v294.1)
G		e5ijzG1	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F:	ECOD (v294.1)
G	HTH_65	e5ijzG2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: HTH_65	ECOD (v294.1)
F		e5ijzF2	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F:	ECOD (v294.1)
F	HTH_65	e5ijzF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: HTH_65	ECOD (v294.1)
E		e5ijzE2	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F:	ECOD (v294.1)
E	HTH_65	e5ijzE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: HTH_65	ECOD (v294.1)
D		e5ijzD1	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F:	ECOD (v294.1)
D	HTH_65	e5ijzD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: HTH_65	ECOD (v294.1)
C		e5ijzC1	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F:	ECOD (v294.1)
C	HTH_65	e5ijzC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: HTH_65	ECOD (v294.1)
B		e5ijzB1	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F:	ECOD (v294.1)
B	HTH_65	e5ijzB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: HTH_65	ECOD (v294.1)
A		e5ijzA1	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F:	ECOD (v294.1)
A	HTH_65	e5ijzA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: HTH_65	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	CATH (4.3.0)
L	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
L	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
J	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	CATH (4.3.0)
J	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
J	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
I	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	CATH (4.3.0)
I	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
I	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	CATH (4.3.0)
H	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	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)
G	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	CATH (4.3.0)
G	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	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)
F	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	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	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	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	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	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	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	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	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	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)
A	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	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)

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, I, J, K, L	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, G, H, I, J, K, L	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, G, H, I, J, K, L	NADP-specific glutamate dehydrogenase	oxidoreductase activity, acting on the CH-NH2 group of donors amino-acid dehydrogenase [NAD(P)+] activity L-glutamate dehydrogenase (NADP+) 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	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006095	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006096	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR050724	Glutamate/Leucine/Phenylalanine/Valine dehydrogenases	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006097	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, dimerisation domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR014362	Glutamate dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR033524	Leu/Phe/Val dehydrogenases active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR033922	NAD(P) binding domain of glutamate dehydrogenase	Domain