Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3BLW

Yeast Isocitrate Dehydrogenase with Citrate and AMP Bound in the Regulatory Subunits

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0003723	molecular_function	RNA binding
A	0003824	molecular_function	catalytic activity
A	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
A	0005515	molecular_function	protein binding
A	0005739	cellular_component	mitochondrion
A	0005758	cellular_component	mitochondrial intermembrane space
A	0005759	cellular_component	mitochondrial matrix
A	0005829	cellular_component	cytosol
A	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
A	0006099	biological_process	tricarboxylic acid cycle
A	0006102	biological_process	isocitrate metabolic process
A	0006537	biological_process	glutamate biosynthetic process
A	0008152	biological_process	metabolic process
A	0016491	molecular_function	oxidoreductase activity
A	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A	0042645	cellular_component	mitochondrial nucleoid
A	0046872	molecular_function	metal ion binding
A	0051287	molecular_function	NAD binding
B	0000287	molecular_function	magnesium ion binding
B	0003723	molecular_function	RNA binding
B	0003824	molecular_function	catalytic activity
B	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
B	0005515	molecular_function	protein binding
B	0005739	cellular_component	mitochondrion
B	0005759	cellular_component	mitochondrial matrix
B	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
B	0006099	biological_process	tricarboxylic acid cycle
B	0006102	biological_process	isocitrate metabolic process
B	0006537	biological_process	glutamate biosynthetic process
B	0008152	biological_process	metabolic process
B	0016491	molecular_function	oxidoreductase activity
B	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B	0046872	molecular_function	metal ion binding
B	0051287	molecular_function	NAD binding
C	0000287	molecular_function	magnesium ion binding
C	0003723	molecular_function	RNA binding
C	0003824	molecular_function	catalytic activity
C	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
C	0005515	molecular_function	protein binding
C	0005739	cellular_component	mitochondrion
C	0005758	cellular_component	mitochondrial intermembrane space
C	0005759	cellular_component	mitochondrial matrix
C	0005829	cellular_component	cytosol
C	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
C	0006099	biological_process	tricarboxylic acid cycle
C	0006102	biological_process	isocitrate metabolic process
C	0006537	biological_process	glutamate biosynthetic process
C	0008152	biological_process	metabolic process
C	0016491	molecular_function	oxidoreductase activity
C	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C	0042645	cellular_component	mitochondrial nucleoid
C	0046872	molecular_function	metal ion binding
C	0051287	molecular_function	NAD binding
D	0000287	molecular_function	magnesium ion binding
D	0003723	molecular_function	RNA binding
D	0003824	molecular_function	catalytic activity
D	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
D	0005515	molecular_function	protein binding
D	0005739	cellular_component	mitochondrion
D	0005759	cellular_component	mitochondrial matrix
D	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
D	0006099	biological_process	tricarboxylic acid cycle
D	0006102	biological_process	isocitrate metabolic process
D	0006537	biological_process	glutamate biosynthetic process
D	0008152	biological_process	metabolic process
D	0016491	molecular_function	oxidoreductase activity
D	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D	0046872	molecular_function	metal ion binding
D	0051287	molecular_function	NAD binding
E	0000287	molecular_function	magnesium ion binding
E	0003723	molecular_function	RNA binding
E	0003824	molecular_function	catalytic activity
E	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
E	0005515	molecular_function	protein binding
E	0005739	cellular_component	mitochondrion
E	0005758	cellular_component	mitochondrial intermembrane space
E	0005759	cellular_component	mitochondrial matrix
E	0005829	cellular_component	cytosol
E	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
E	0006099	biological_process	tricarboxylic acid cycle
E	0006102	biological_process	isocitrate metabolic process
E	0006537	biological_process	glutamate biosynthetic process
E	0008152	biological_process	metabolic process
E	0016491	molecular_function	oxidoreductase activity
E	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
E	0042645	cellular_component	mitochondrial nucleoid
E	0046872	molecular_function	metal ion binding
E	0051287	molecular_function	NAD binding
F	0000287	molecular_function	magnesium ion binding
F	0003723	molecular_function	RNA binding
F	0003824	molecular_function	catalytic activity
F	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
F	0005515	molecular_function	protein binding
F	0005739	cellular_component	mitochondrion
F	0005759	cellular_component	mitochondrial matrix
F	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
F	0006099	biological_process	tricarboxylic acid cycle
F	0006102	biological_process	isocitrate metabolic process
F	0006537	biological_process	glutamate biosynthetic process
F	0008152	biological_process	metabolic process
F	0016491	molecular_function	oxidoreductase activity
F	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
F	0046872	molecular_function	metal ion binding
F	0051287	molecular_function	NAD binding
G	0000287	molecular_function	magnesium ion binding
G	0003723	molecular_function	RNA binding
G	0003824	molecular_function	catalytic activity
G	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
G	0005515	molecular_function	protein binding
G	0005739	cellular_component	mitochondrion
G	0005758	cellular_component	mitochondrial intermembrane space
G	0005759	cellular_component	mitochondrial matrix
G	0005829	cellular_component	cytosol
G	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
G	0006099	biological_process	tricarboxylic acid cycle
G	0006102	biological_process	isocitrate metabolic process
G	0006537	biological_process	glutamate biosynthetic process
G	0008152	biological_process	metabolic process
G	0016491	molecular_function	oxidoreductase activity
G	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
G	0042645	cellular_component	mitochondrial nucleoid
G	0046872	molecular_function	metal ion binding
G	0051287	molecular_function	NAD binding
H	0000287	molecular_function	magnesium ion binding
H	0003723	molecular_function	RNA binding
H	0003824	molecular_function	catalytic activity
H	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
H	0005515	molecular_function	protein binding
H	0005739	cellular_component	mitochondrion
H	0005759	cellular_component	mitochondrial matrix
H	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
H	0006099	biological_process	tricarboxylic acid cycle
H	0006102	biological_process	isocitrate metabolic process
H	0006537	biological_process	glutamate biosynthetic process
H	0008152	biological_process	metabolic process
H	0016491	molecular_function	oxidoreductase activity
H	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
H	0046872	molecular_function	metal ion binding
H	0051287	molecular_function	NAD binding
I	0000287	molecular_function	magnesium ion binding
I	0003723	molecular_function	RNA binding
I	0003824	molecular_function	catalytic activity
I	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
I	0005515	molecular_function	protein binding
I	0005739	cellular_component	mitochondrion
I	0005758	cellular_component	mitochondrial intermembrane space
I	0005759	cellular_component	mitochondrial matrix
I	0005829	cellular_component	cytosol
I	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
I	0006099	biological_process	tricarboxylic acid cycle
I	0006102	biological_process	isocitrate metabolic process
I	0006537	biological_process	glutamate biosynthetic process
I	0008152	biological_process	metabolic process
I	0016491	molecular_function	oxidoreductase activity
I	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
I	0042645	cellular_component	mitochondrial nucleoid
I	0046872	molecular_function	metal ion binding
I	0051287	molecular_function	NAD binding
J	0000287	molecular_function	magnesium ion binding
J	0003723	molecular_function	RNA binding
J	0003824	molecular_function	catalytic activity
J	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
J	0005515	molecular_function	protein binding
J	0005739	cellular_component	mitochondrion
J	0005759	cellular_component	mitochondrial matrix
J	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
J	0006099	biological_process	tricarboxylic acid cycle
J	0006102	biological_process	isocitrate metabolic process
J	0006537	biological_process	glutamate biosynthetic process
J	0008152	biological_process	metabolic process
J	0016491	molecular_function	oxidoreductase activity
J	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
J	0046872	molecular_function	metal ion binding
J	0051287	molecular_function	NAD binding
K	0000287	molecular_function	magnesium ion binding
K	0003723	molecular_function	RNA binding
K	0003824	molecular_function	catalytic activity
K	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
K	0005515	molecular_function	protein binding
K	0005739	cellular_component	mitochondrion
K	0005758	cellular_component	mitochondrial intermembrane space
K	0005759	cellular_component	mitochondrial matrix
K	0005829	cellular_component	cytosol
K	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
K	0006099	biological_process	tricarboxylic acid cycle
K	0006102	biological_process	isocitrate metabolic process
K	0006537	biological_process	glutamate biosynthetic process
K	0008152	biological_process	metabolic process
K	0016491	molecular_function	oxidoreductase activity
K	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
K	0042645	cellular_component	mitochondrial nucleoid
K	0046872	molecular_function	metal ion binding
K	0051287	molecular_function	NAD binding
L	0000287	molecular_function	magnesium ion binding
L	0003723	molecular_function	RNA binding
L	0003824	molecular_function	catalytic activity
L	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
L	0005515	molecular_function	protein binding
L	0005739	cellular_component	mitochondrion
L	0005759	cellular_component	mitochondrial matrix
L	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
L	0006099	biological_process	tricarboxylic acid cycle
L	0006102	biological_process	isocitrate metabolic process
L	0006537	biological_process	glutamate biosynthetic process
L	0008152	biological_process	metabolic process
L	0016491	molecular_function	oxidoreductase activity
L	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
L	0046872	molecular_function	metal ion binding
L	0051287	molecular_function	NAD binding
M	0000287	molecular_function	magnesium ion binding
M	0003723	molecular_function	RNA binding
M	0003824	molecular_function	catalytic activity
M	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
M	0005515	molecular_function	protein binding
M	0005739	cellular_component	mitochondrion
M	0005758	cellular_component	mitochondrial intermembrane space
M	0005759	cellular_component	mitochondrial matrix
M	0005829	cellular_component	cytosol
M	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
M	0006099	biological_process	tricarboxylic acid cycle
M	0006102	biological_process	isocitrate metabolic process
M	0006537	biological_process	glutamate biosynthetic process
M	0008152	biological_process	metabolic process
M	0016491	molecular_function	oxidoreductase activity
M	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
M	0042645	cellular_component	mitochondrial nucleoid
M	0046872	molecular_function	metal ion binding
M	0051287	molecular_function	NAD binding
N	0000287	molecular_function	magnesium ion binding
N	0003723	molecular_function	RNA binding
N	0003824	molecular_function	catalytic activity
N	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
N	0005515	molecular_function	protein binding
N	0005739	cellular_component	mitochondrion
N	0005759	cellular_component	mitochondrial matrix
N	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
N	0006099	biological_process	tricarboxylic acid cycle
N	0006102	biological_process	isocitrate metabolic process
N	0006537	biological_process	glutamate biosynthetic process
N	0008152	biological_process	metabolic process
N	0016491	molecular_function	oxidoreductase activity
N	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
N	0046872	molecular_function	metal ion binding
N	0051287	molecular_function	NAD binding
O	0000287	molecular_function	magnesium ion binding
O	0003723	molecular_function	RNA binding
O	0003824	molecular_function	catalytic activity
O	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
O	0005515	molecular_function	protein binding
O	0005739	cellular_component	mitochondrion
O	0005758	cellular_component	mitochondrial intermembrane space
O	0005759	cellular_component	mitochondrial matrix
O	0005829	cellular_component	cytosol
O	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
O	0006099	biological_process	tricarboxylic acid cycle
O	0006102	biological_process	isocitrate metabolic process
O	0006537	biological_process	glutamate biosynthetic process
O	0008152	biological_process	metabolic process
O	0016491	molecular_function	oxidoreductase activity
O	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
O	0042645	cellular_component	mitochondrial nucleoid
O	0046872	molecular_function	metal ion binding
O	0051287	molecular_function	NAD binding
P	0000287	molecular_function	magnesium ion binding
P	0003723	molecular_function	RNA binding
P	0003824	molecular_function	catalytic activity
P	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
P	0005515	molecular_function	protein binding
P	0005739	cellular_component	mitochondrion
P	0005759	cellular_component	mitochondrial matrix
P	0005962	cellular_component	obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
P	0006099	biological_process	tricarboxylic acid cycle
P	0006102	biological_process	isocitrate metabolic process
P	0006537	biological_process	glutamate biosynthetic process
P	0008152	biological_process	metabolic process
P	0016491	molecular_function	oxidoreductase activity
P	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
P	0046872	molecular_function	metal ion binding
P	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FLC A 1001

Chain	Residue
A	THR83
B	LYS189
A	SER92
A	ASN94
A	VAL95
A	ARG98
A	ARG129
A	PHE136
A	THR241
A	ARG274

site_id	AC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FLC C 1002

Chain	Residue
C	THR83
C	SER92
C	ASN94
C	VAL95
C	ARG98
C	ARG129
C	PHE136
C	THR241
C	ARG274
D	LYS189

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FLC E 1003

Chain	Residue
E	THR83
E	SER92
E	ARG98
E	ARG129
E	PHE136
E	THR241
E	ARG274
F	LYS189
F	THR191
F	ASP222

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FLC G 1004

Chain	Residue
G	THR83
G	SER92
G	VAL95
G	ARG98
G	ARG129
G	PHE136
G	THR241
G	ARG274
H	LYS189
H	THR191

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FLC I 1005

Chain	Residue
I	THR83
I	SER92
I	VAL95
I	ARG98
I	ARG129
I	PHE136
I	THR241
I	ARG274
J	LYS189

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FLC K 1006

Chain	Residue
K	THR83
K	SER92
K	ARG98
K	ARG129
K	PHE136
K	THR241
K	ARG274
L	LYS189
L	ASP222

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FLC M 1007

Chain	Residue
M	THR83
M	SER92
M	ASN94
M	VAL95
M	ARG98
M	PHE136
M	THR241
M	ARG274
N	LYS189

site_id	AC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FLC O 1008

Chain	Residue
O	THR83
O	SER92
O	ASN94
O	ARG98
O	ARG129
O	PHE136
O	THR241
O	ARG274
P	LYS189

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE AMP A 2001

Chain	Residue
A	HIS275
A	GLY277
A	ALA286
A	ASN287
A	ASP328
B	ASN223

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE AMP C 2002

Chain	Residue
C	VAL28
C	ILE32
C	GLY255
C	HIS275
C	VAL276
C	GLY277
C	ASN287
D	ASN223

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP E 2003

Chain	Residue
E	VAL28
E	HIS275
E	GLY277
E	ASN287
F	ASN223

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE AMP G 2004

Chain	Residue
G	ASN287
G	ASP328
H	ASN223
G	VAL28
G	HIS275
G	GLY277
G	ALA286

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE AMP I 2005

Chain	Residue
I	HIS275
I	GLY277
I	ALA286
I	ASN287
I	ASP328
J	ASN223

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE AMP K 2006

Chain	Residue
K	VAL28
K	HIS275
K	VAL276
K	GLY277
K	ALA286
L	ASN223

site_id	BC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE AMP M 2007

Chain	Residue
M	ILE32
M	GLY255
M	HIS275
M	VAL276
M	GLY277
M	ASP279
M	ASN287
N	ASN223

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE AMP O 2008

Chain	Residue
O	VAL28
O	HIS275
O	VAL276
O	GLY277
O	ASN287
O	ASP328
P	ASN223

Functional Information from PROSITE/UniProt

site_id	PS00470
Number of Residues	20
Details	IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. SMYGTIlGNigAali.GGPGL

Chain	Residue	Details
A	SER237-LEU256
B	ASN244-LEU264

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	32
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
N	ARG104
N	ARG114
N	ARG135
N	ASP222
P	ARG104
P	ARG114
P	ARG135
P	ASP222
B	ARG104
B	ARG114
B	ARG135
B	ASP222
D	ARG104
D	ARG114
D	ARG135
D	ASP222
F	ARG104
F	ARG114
F	ARG135
F	ASP222
H	ARG104
H	ARG114
H	ARG135
H	ASP222
J	ARG104
J	ARG114
J	ARG135
J	ASP222
L	ARG104
L	ARG114
L	ARG135
L	ASP222

site_id	SWS_FT_FI2
Number of Residues	16
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P50213

Chain	Residue	Details
B	ASP248
B	ASP252
D	ASP248
D	ASP252
F	ASP248
F	ASP252
H	ASP248
H	ASP252
J	ASP248
J	ASP252
L	ASP248
L	ASP252
N	ASP248
N	ASP252
P	ASP248
P	ASP252

site_id	SWS_FT_FI3
Number of Residues	16
Details	SITE: Critical for catalysis => ECO:0000250

Chain	Residue	Details
B	TYR142
B	LYS189
D	TYR142
D	LYS189
F	TYR142
F	LYS189
H	TYR142
H	LYS189
J	TYR142
J	LYS189
L	TYR142
L	LYS189
N	TYR142
N	LYS189
P	TYR142
P	LYS189

site_id	SWS_FT_FI4
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:18407956

Chain	Residue	Details
B	THR90
D	THR90
F	THR90
H	THR90
J	THR90
L	THR90
N	THR90
P	THR90

site_id	SWS_FT_FI5
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:18407956, ECO:0007744\|PubMed:19779198

Chain	Residue	Details
B	THR138
D	THR138
F	THR138
H	THR138
J	THR138
L	THR138
N	THR138
P	THR138

site_id	SWS_FT_FI6
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:19779198

Chain	Residue	Details
B	THR312
D	THR312
F	THR312
H	THR312
J	THR312
L	THR312
N	THR312
P	THR312

site_id	SWS_FT_FI7
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:17761666

Chain	Residue	Details
B	THR334
D	THR334
F	THR334
H	THR334
J	THR334
L	THR334
N	THR334
P	THR334

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)