Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2QFX

Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with NADPH, a-ketoglutarate and Ca(2+)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
A	0005515	molecular_function	protein binding
A	0005739	cellular_component	mitochondrion
A	0006097	biological_process	glyoxylate cycle
A	0006099	biological_process	tricarboxylic acid cycle
A	0006102	biological_process	isocitrate metabolic process
A	0006537	biological_process	glutamate biosynthetic process
A	0006739	biological_process	NADP 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	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
B	0005515	molecular_function	protein binding
B	0005739	cellular_component	mitochondrion
B	0006097	biological_process	glyoxylate cycle
B	0006099	biological_process	tricarboxylic acid cycle
B	0006102	biological_process	isocitrate metabolic process
B	0006537	biological_process	glutamate biosynthetic process
B	0006739	biological_process	NADP 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	0042645	cellular_component	mitochondrial nucleoid
B	0046872	molecular_function	metal ion binding
B	0051287	molecular_function	NAD binding
C	0000287	molecular_function	magnesium ion binding
C	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
C	0005515	molecular_function	protein binding
C	0005739	cellular_component	mitochondrion
C	0006097	biological_process	glyoxylate cycle
C	0006099	biological_process	tricarboxylic acid cycle
C	0006102	biological_process	isocitrate metabolic process
C	0006537	biological_process	glutamate biosynthetic process
C	0006739	biological_process	NADP 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	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
D	0005515	molecular_function	protein binding
D	0005739	cellular_component	mitochondrion
D	0006097	biological_process	glyoxylate cycle
D	0006099	biological_process	tricarboxylic acid cycle
D	0006102	biological_process	isocitrate metabolic process
D	0006537	biological_process	glutamate biosynthetic process
D	0006739	biological_process	NADP 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	0042645	cellular_component	mitochondrial nucleoid
D	0046872	molecular_function	metal ion binding
D	0051287	molecular_function	NAD binding
E	0000287	molecular_function	magnesium ion binding
E	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
E	0005515	molecular_function	protein binding
E	0005739	cellular_component	mitochondrion
E	0006097	biological_process	glyoxylate cycle
E	0006099	biological_process	tricarboxylic acid cycle
E	0006102	biological_process	isocitrate metabolic process
E	0006537	biological_process	glutamate biosynthetic process
E	0006739	biological_process	NADP 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	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
F	0005515	molecular_function	protein binding
F	0005739	cellular_component	mitochondrion
F	0006097	biological_process	glyoxylate cycle
F	0006099	biological_process	tricarboxylic acid cycle
F	0006102	biological_process	isocitrate metabolic process
F	0006537	biological_process	glutamate biosynthetic process
F	0006739	biological_process	NADP 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	0042645	cellular_component	mitochondrial nucleoid
F	0046872	molecular_function	metal ion binding
F	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA A 1103

Chain	Residue
A	ASP277
A	ASP281
B	ASP254

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA B 1203

Chain	Residue
A	ASP254
B	ASP277
B	ASP281

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA C 1303

Chain	Residue
C	HOH1306
D	ASP254
C	ARG110
C	ASP277
C	ASP281

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA D 1403

Chain	Residue
C	ASP254
D	ASP277
D	ASP281

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA E 1503

Chain	Residue
E	ASP277
E	ASP281
F	ASP254

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA F 1603

Chain	Residue
E	ASP254
F	ASP277
F	ASP281

site_id	AC7
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NDP A 1101

Chain	Residue
A	LYS73
A	ALA75
A	THR76
A	ILE77
A	THR78
A	ARG83
A	ASN97
A	LEU290
A	HIS311
A	GLY312
A	THR313
A	THR315
A	ARG316
A	HIS317
A	ASN330
A	HOH1106
A	HOH1113
A	HOH1116
A	HOH1120
B	ASP255
B	GLN259
B	LYS262

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE AKG A 1102

Chain	Residue
A	THR78
A	SER95
A	ASN97
A	ARG101
A	ARG110
A	ASP277
A	ALA310
A	HOH1120
A	HOH1123
B	ASP254

site_id	AC9
Number of Residues	17
Details	BINDING SITE FOR RESIDUE NDP B 1201

Chain	Residue
A	GLN259
A	LYS262
B	LYS73
B	ALA75
B	THR76
B	ILE77
B	THR78
B	ARG83
B	ASN97
B	LEU290
B	HIS311
B	GLY312
B	THR313
B	THR315
B	ARG316
B	HIS317
B	ASN330

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE AKG B 1202

Chain	Residue
A	LYS214
A	ASP254
B	THR78
B	SER95
B	ASN97
B	ARG101
B	ARG110
B	ALA310

site_id	BC2
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NDP C 1301

Chain	Residue
C	LYS73
C	ALA75
C	THR76
C	ILE77
C	THR78
C	ARG83
C	ASN97
C	LEU290
C	HIS311
C	GLY312
C	THR313
C	THR315
C	ARG316
C	HIS317
C	THR329
C	ASN330
C	HOH1308
C	HOH1319
C	HOH1329
D	LEU252
D	GLN259
D	LYS262

site_id	BC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE AKG C 1302

Chain	Residue
C	THR78
C	SER95
C	ASN97
C	ARG101
C	ARG110
C	ARG133
C	ALA310
C	HOH1306
C	HOH1329
D	ASP254

site_id	BC4
Number of Residues	21
Details	BINDING SITE FOR RESIDUE NDP D 1401

Chain	Residue
C	ASP255
C	GLN259
C	LYS262
C	HOH1311
D	LYS73
D	ALA75
D	THR76
D	ILE77
D	THR78
D	ARG83
D	ASN97
D	LEU290
D	GLU308
D	HIS311
D	GLY312
D	THR313
D	THR315
D	ARG316
D	HIS317
D	ASN330
D	HOH1415

site_id	BC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE AKG D 1402

Chain	Residue
C	ASP254
D	THR78
D	SER95
D	ASN97
D	ARG101
D	ARG110
D	ARG133
D	ASP277

site_id	BC6
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NDP E 1501

Chain	Residue
E	LYS73
E	ALA75
E	THR76
E	ILE77
E	THR78
E	ARG83
E	ASN97
E	LEU290
E	HIS311
E	GLY312
E	THR313
E	THR315
E	ARG316
E	HIS317
E	ASN330
E	HOH1506
E	HOH1513
F	LEU252
F	ASP255
F	GLN259
F	LYS262
F	HOH1612

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE AKG E 1502

Chain	Residue
E	THR78
E	SER95
E	ARG101
E	ARG110
E	ARG133
E	ASP277
F	ASP254

site_id	BC8
Number of Residues	19
Details	BINDING SITE FOR RESIDUE NDP F 1601

Chain	Residue
E	ASP255
E	GLN259
E	LYS262
F	LYS73
F	ALA75
F	THR76
F	ILE77
F	THR78
F	ARG83
F	ASN97
F	LEU290
F	HIS311
F	GLY312
F	THR313
F	THR315
F	ARG316
F	HIS317
F	ASN330
F	HOH1609

site_id	BC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE AKG F 1602

Chain	Residue
E	ASP254
F	THR78
F	SER95
F	ASN97
F	ARG101
F	ARG110
F	ARG133
F	ASP277
F	HOH1618

Functional Information from PROSITE/UniProt

site_id	PS00470
Number of Residues	20
Details	IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NYDGDVqSDivAqgf.GSLGL

Chain	Residue	Details
A	ASN273-LEU292

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	66
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	THR76
A	GLY312
A	ASN330
B	THR76
B	THR78
B	ARG83
B	SER95
B	ARG110
B	ARG133
B	ASP254
B	LYS262
A	THR78
B	ASP277
B	GLY312
B	ASN330
C	THR76
C	THR78
C	ARG83
C	SER95
C	ARG110
C	ARG133
C	ASP254
A	ARG83
C	LYS262
C	ASP277
C	GLY312
C	ASN330
D	THR76
D	THR78
D	ARG83
D	SER95
D	ARG110
D	ARG133
A	SER95
D	ASP254
D	LYS262
D	ASP277
D	GLY312
D	ASN330
E	THR76
E	THR78
E	ARG83
E	SER95
E	ARG110
A	ARG110
E	ARG133
E	ASP254
E	LYS262
E	ASP277
E	GLY312
E	ASN330
F	THR76
F	THR78
F	ARG83
F	SER95
A	ARG133
F	ARG110
F	ARG133
F	ASP254
F	LYS262
F	ASP277
F	GLY312
F	ASN330
A	ASP254
A	LYS262
A	ASP277

site_id	SWS_FT_FI2
Number of Residues	12
Details	SITE: Critical for catalysis => ECO:0000250

Chain	Residue	Details
A	TYR140
E	LYS214
F	TYR140
F	LYS214
A	LYS214
B	TYR140
B	LYS214
C	TYR140
C	LYS214
D	TYR140
D	LYS214
E	TYR140

Catalytic Information from CSA

site_id	CSA1
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
A	VAL156

site_id	CSA10
Number of Residues	2
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
D	ASP254
D	LYS214

site_id	CSA11
Number of Residues	2
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
E	ASP254
E	LYS214

site_id	CSA12
Number of Residues	2
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
F	ASP254
F	LYS214

site_id	CSA13
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
A	THR163

site_id	CSA14
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
B	THR163

site_id	CSA15
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
C	THR163

site_id	CSA16
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
D	THR163

site_id	CSA17
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
E	THR163

site_id	CSA18
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
F	THR163

site_id	CSA2
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
B	VAL156

site_id	CSA3
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
C	VAL156

site_id	CSA4
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
D	VAL156

site_id	CSA5
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
E	VAL156

site_id	CSA6
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
F	VAL156

site_id	CSA7
Number of Residues	2
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
A	ASP254
A	LYS214

site_id	CSA8
Number of Residues	2
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
B	ASP254
B	LYS214

site_id	CSA9
Number of Residues	2
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
C	ASP254
C	LYS214

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