Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3JD3

Glutamate dehydrogenase in complex with NADH and GTP, open conformation

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004352	molecular_function	glutamate dehydrogenase (NAD+) activity
A	0004353	molecular_function	glutamate dehydrogenase [NAD(P)+] activity
A	0004354	molecular_function	glutamate dehydrogenase (NADP+) activity
A	0005524	molecular_function	ATP binding
A	0005525	molecular_function	GTP binding
A	0005739	cellular_component	mitochondrion
A	0005743	cellular_component	mitochondrial inner membrane
A	0005783	cellular_component	endoplasmic reticulum
A	0006520	biological_process	amino acid metabolic process
A	0006538	biological_process	L-glutamate catabolic process
A	0006541	biological_process	glutamine metabolic process
A	0016491	molecular_function	oxidoreductase activity
A	0016639	molecular_function	oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
A	0042802	molecular_function	identical protein binding
A	0072350	biological_process	tricarboxylic acid metabolic process
B	0000166	molecular_function	nucleotide binding
B	0004352	molecular_function	glutamate dehydrogenase (NAD+) activity
B	0004353	molecular_function	glutamate dehydrogenase [NAD(P)+] activity
B	0004354	molecular_function	glutamate dehydrogenase (NADP+) activity
B	0005524	molecular_function	ATP binding
B	0005525	molecular_function	GTP binding
B	0005739	cellular_component	mitochondrion
B	0005743	cellular_component	mitochondrial inner membrane
B	0005783	cellular_component	endoplasmic reticulum
B	0006520	biological_process	amino acid metabolic process
B	0006538	biological_process	L-glutamate catabolic process
B	0006541	biological_process	glutamine metabolic process
B	0016491	molecular_function	oxidoreductase activity
B	0016639	molecular_function	oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
B	0042802	molecular_function	identical protein binding
B	0072350	biological_process	tricarboxylic acid metabolic process
C	0000166	molecular_function	nucleotide binding
C	0004352	molecular_function	glutamate dehydrogenase (NAD+) activity
C	0004353	molecular_function	glutamate dehydrogenase [NAD(P)+] activity
C	0004354	molecular_function	glutamate dehydrogenase (NADP+) activity
C	0005524	molecular_function	ATP binding
C	0005525	molecular_function	GTP binding
C	0005739	cellular_component	mitochondrion
C	0005743	cellular_component	mitochondrial inner membrane
C	0005783	cellular_component	endoplasmic reticulum
C	0006520	biological_process	amino acid metabolic process
C	0006538	biological_process	L-glutamate catabolic process
C	0006541	biological_process	glutamine metabolic process
C	0016491	molecular_function	oxidoreductase activity
C	0016639	molecular_function	oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
C	0042802	molecular_function	identical protein binding
C	0072350	biological_process	tricarboxylic acid metabolic process
D	0000166	molecular_function	nucleotide binding
D	0004352	molecular_function	glutamate dehydrogenase (NAD+) activity
D	0004353	molecular_function	glutamate dehydrogenase [NAD(P)+] activity
D	0004354	molecular_function	glutamate dehydrogenase (NADP+) activity
D	0005524	molecular_function	ATP binding
D	0005525	molecular_function	GTP binding
D	0005739	cellular_component	mitochondrion
D	0005743	cellular_component	mitochondrial inner membrane
D	0005783	cellular_component	endoplasmic reticulum
D	0006520	biological_process	amino acid metabolic process
D	0006538	biological_process	L-glutamate catabolic process
D	0006541	biological_process	glutamine metabolic process
D	0016491	molecular_function	oxidoreductase activity
D	0016639	molecular_function	oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
D	0042802	molecular_function	identical protein binding
D	0072350	biological_process	tricarboxylic acid metabolic process
E	0000166	molecular_function	nucleotide binding
E	0004352	molecular_function	glutamate dehydrogenase (NAD+) activity
E	0004353	molecular_function	glutamate dehydrogenase [NAD(P)+] activity
E	0004354	molecular_function	glutamate dehydrogenase (NADP+) activity
E	0005524	molecular_function	ATP binding
E	0005525	molecular_function	GTP binding
E	0005739	cellular_component	mitochondrion
E	0005743	cellular_component	mitochondrial inner membrane
E	0005783	cellular_component	endoplasmic reticulum
E	0006520	biological_process	amino acid metabolic process
E	0006538	biological_process	L-glutamate catabolic process
E	0006541	biological_process	glutamine metabolic process
E	0016491	molecular_function	oxidoreductase activity
E	0016639	molecular_function	oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
E	0042802	molecular_function	identical protein binding
E	0072350	biological_process	tricarboxylic acid metabolic process
F	0000166	molecular_function	nucleotide binding
F	0004352	molecular_function	glutamate dehydrogenase (NAD+) activity
F	0004353	molecular_function	glutamate dehydrogenase [NAD(P)+] activity
F	0004354	molecular_function	glutamate dehydrogenase (NADP+) activity
F	0005524	molecular_function	ATP binding
F	0005525	molecular_function	GTP binding
F	0005739	cellular_component	mitochondrion
F	0005743	cellular_component	mitochondrial inner membrane
F	0005783	cellular_component	endoplasmic reticulum
F	0006520	biological_process	amino acid metabolic process
F	0006538	biological_process	L-glutamate catabolic process
F	0006541	biological_process	glutamine metabolic process
F	0016491	molecular_function	oxidoreductase activity
F	0016639	molecular_function	oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
F	0042802	molecular_function	identical protein binding
F	0072350	biological_process	tricarboxylic acid metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GTP A 601

Chain	Residue
A	ARG261
A	TYR262
A	GLU292
A	LYS446
A	HIS450

site_id	AC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE NAI A 602

Chain	Residue
A	ASN254
A	GLU275
A	SER276
A	ALA326
A	GLN330
A	ALA348
A	MET169
A	GLN250
A	PHE252
A	GLY253

site_id	AC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE NAI A 603

Chain	Residue
A	HIS85
A	ARG86
A	CYS115
A	ASP119
A	VAL120
A	PHE122
A	ARG459
A	GLN463
B	SER204
B	HIS209
B	SER393
B	SER444
B	GLU445

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GTP B 601

Chain	Residue
B	ARG261
B	TYR262
B	GLU292
B	LYS446
B	HIS450

site_id	AC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE NAI B 602

Chain	Residue
B	MET169
B	GLN250
B	PHE252
B	GLY253
B	ASN254
B	GLU275
B	SER276
B	ALA326
B	GLN330
B	ALA348

site_id	AC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE NAI B 603

Chain	Residue
B	HIS85
B	ARG86
B	CYS115
B	ASP119
B	VAL120
B	PHE122
B	ARG459
B	GLN463
C	SER204
C	HIS209
C	SER393
C	SER444
C	GLU445

site_id	AC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE NAI C 601

Chain	Residue
A	SER204
A	HIS209
A	SER393
A	SER444
A	GLU445
C	HIS85
C	ARG86
C	CYS115
C	ASP119
C	VAL120
C	PHE122
C	ARG459
C	GLN463

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GTP C 602

Chain	Residue
C	ARG261
C	TYR262
C	GLU292
C	LYS446
C	HIS450

site_id	AC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE NAI C 603

Chain	Residue
C	MET169
C	GLN250
C	PHE252
C	GLY253
C	ASN254
C	GLU275
C	SER276
C	ALA326
C	GLN330
C	ALA348

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GTP D 601

Chain	Residue
D	ARG261
D	TYR262
D	GLU292
D	LYS446
D	HIS450

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE NAI D 602

Chain	Residue
D	MET169
D	GLN250
D	PHE252
D	GLY253
D	ASN254
D	GLU275
D	SER276
D	ALA326
D	GLN330
D	ALA348

site_id	BC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE NAI D 603

Chain	Residue
D	HIS85
D	ARG86
D	CYS115
D	ASP119
D	VAL120
D	PHE122
D	ARG459
D	GLN463
E	SER204
E	HIS209
E	SER393
E	SER444
E	GLU445

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GTP E 601

Chain	Residue
E	ARG261
E	TYR262
E	GLU292
E	LYS446
E	HIS450

site_id	BC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE NAI E 602

Chain	Residue
E	MET169
E	GLN250
E	PHE252
E	GLY253
E	ASN254
E	GLU275
E	SER276
E	ALA326
E	GLN330
E	ALA348

site_id	BC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE NAI E 603

Chain	Residue
E	HIS85
E	ARG86
E	CYS115
E	ASP119
E	VAL120
E	PHE122
E	ARG459
E	GLN463
F	SER204
F	HIS209
F	SER393
F	SER444
F	GLU445

site_id	BC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE NAI F 601

Chain	Residue
D	SER204
D	HIS209
D	SER393
D	SER444
D	GLU445
F	HIS85
F	ARG86
F	CYS115
F	ASP119
F	VAL120
F	PHE122
F	ARG459
F	GLN463

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GTP F 602

Chain	Residue
F	ARG261
F	TYR262
F	GLU292
F	LYS446
F	HIS450

site_id	BC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE NAI F 603

Chain	Residue
F	MET169
F	GLN250
F	PHE252
F	GLY253
F	ASN254
F	GLU275
F	SER276
F	ALA326
F	GLN330
F	ALA348

Functional Information from PROSITE/UniProt

site_id	PS00074
Number of Residues	14
Details	GLFV_DEHYDROGENASE Glu / Leu / Phe / Val dehydrogenases active site. VpfGGAKaGvkiNP

Chain	Residue	Details
A	VAL120-PRO133

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU10011","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	72
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11254391","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12653548","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	12
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P26443","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	12
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P26443","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	54
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22076378","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	18
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"22076378","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	6
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P26443","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	6
Details	Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"UniProtKB","id":"P00367","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	24
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P26443","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	6
Details	Modified residue: {"description":"ADP-ribosylcysteine","evidences":[{"source":"UniProtKB","id":"P00367","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	48
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P26443","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	12
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P00367","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	6
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P10860","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	6
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P00367","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)