Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8GS5

Crystal structure of a constitutively active mutant of human IDH3 holoenzyme in apo form

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005739	cellular_component	mitochondrion
A	0005759	cellular_component	mitochondrial matrix
A	0005975	biological_process	carbohydrate metabolic process
A	0006099	biological_process	tricarboxylic acid cycle
A	0006102	biological_process	isocitrate 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	0046872	molecular_function	metal ion binding
A	0051287	molecular_function	NAD binding
B	0000287	molecular_function	magnesium ion binding
B	0006099	biological_process	tricarboxylic acid cycle
B	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B	0051287	molecular_function	NAD binding
C	0000287	molecular_function	magnesium ion binding
C	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005739	cellular_component	mitochondrion
C	0005759	cellular_component	mitochondrial matrix
C	0005975	biological_process	carbohydrate metabolic process
C	0006099	biological_process	tricarboxylic acid cycle
C	0006102	biological_process	isocitrate 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	0046872	molecular_function	metal ion binding
C	0051287	molecular_function	NAD binding
D	0000287	molecular_function	magnesium ion binding
D	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005730	cellular_component	nucleolus
D	0005739	cellular_component	mitochondrion
D	0005759	cellular_component	mitochondrial matrix
D	0005975	biological_process	carbohydrate metabolic process
D	0006099	biological_process	tricarboxylic acid cycle
D	0006102	biological_process	isocitrate metabolic process
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	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005739	cellular_component	mitochondrion
E	0005759	cellular_component	mitochondrial matrix
E	0005975	biological_process	carbohydrate metabolic process
E	0006099	biological_process	tricarboxylic acid cycle
E	0006102	biological_process	isocitrate 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	0046872	molecular_function	metal ion binding
E	0051287	molecular_function	NAD binding
F	0000287	molecular_function	magnesium ion binding
F	0006099	biological_process	tricarboxylic acid cycle
F	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
F	0051287	molecular_function	NAD binding
G	0000287	molecular_function	magnesium ion binding
G	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005739	cellular_component	mitochondrion
G	0005759	cellular_component	mitochondrial matrix
G	0005975	biological_process	carbohydrate metabolic process
G	0006099	biological_process	tricarboxylic acid cycle
G	0006102	biological_process	isocitrate 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	0046872	molecular_function	metal ion binding
G	0051287	molecular_function	NAD binding
H	0000287	molecular_function	magnesium ion binding
H	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
H	0005515	molecular_function	protein binding
H	0005524	molecular_function	ATP binding
H	0005730	cellular_component	nucleolus
H	0005739	cellular_component	mitochondrion
H	0005759	cellular_component	mitochondrial matrix
H	0005975	biological_process	carbohydrate metabolic process
H	0006099	biological_process	tricarboxylic acid cycle
H	0006102	biological_process	isocitrate metabolic process
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	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005739	cellular_component	mitochondrion
I	0005759	cellular_component	mitochondrial matrix
I	0005975	biological_process	carbohydrate metabolic process
I	0006099	biological_process	tricarboxylic acid cycle
I	0006102	biological_process	isocitrate 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	0046872	molecular_function	metal ion binding
I	0051287	molecular_function	NAD binding
J	0000287	molecular_function	magnesium ion binding
J	0006099	biological_process	tricarboxylic acid cycle
J	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
J	0051287	molecular_function	NAD binding
K	0000287	molecular_function	magnesium ion binding
K	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005739	cellular_component	mitochondrion
K	0005759	cellular_component	mitochondrial matrix
K	0005975	biological_process	carbohydrate metabolic process
K	0006099	biological_process	tricarboxylic acid cycle
K	0006102	biological_process	isocitrate 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	0046872	molecular_function	metal ion binding
K	0051287	molecular_function	NAD binding
L	0000287	molecular_function	magnesium ion binding
L	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
L	0005515	molecular_function	protein binding
L	0005524	molecular_function	ATP binding
L	0005730	cellular_component	nucleolus
L	0005739	cellular_component	mitochondrion
L	0005759	cellular_component	mitochondrial matrix
L	0005975	biological_process	carbohydrate metabolic process
L	0006099	biological_process	tricarboxylic acid cycle
L	0006102	biological_process	isocitrate metabolic process
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	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
M	0005515	molecular_function	protein binding
M	0005634	cellular_component	nucleus
M	0005739	cellular_component	mitochondrion
M	0005759	cellular_component	mitochondrial matrix
M	0005975	biological_process	carbohydrate metabolic process
M	0006099	biological_process	tricarboxylic acid cycle
M	0006102	biological_process	isocitrate 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	0046872	molecular_function	metal ion binding
M	0051287	molecular_function	NAD binding
N	0000287	molecular_function	magnesium ion binding
N	0006099	biological_process	tricarboxylic acid cycle
N	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
N	0051287	molecular_function	NAD binding
O	0000287	molecular_function	magnesium ion binding
O	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
O	0005515	molecular_function	protein binding
O	0005634	cellular_component	nucleus
O	0005739	cellular_component	mitochondrion
O	0005759	cellular_component	mitochondrial matrix
O	0005975	biological_process	carbohydrate metabolic process
O	0006099	biological_process	tricarboxylic acid cycle
O	0006102	biological_process	isocitrate 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	0046872	molecular_function	metal ion binding
O	0051287	molecular_function	NAD binding
P	0000287	molecular_function	magnesium ion binding
P	0004449	molecular_function	isocitrate dehydrogenase (NAD+) activity
P	0005515	molecular_function	protein binding
P	0005524	molecular_function	ATP binding
P	0005730	cellular_component	nucleolus
P	0005739	cellular_component	mitochondrion
P	0005759	cellular_component	mitochondrial matrix
P	0005975	biological_process	carbohydrate metabolic process
P	0006099	biological_process	tricarboxylic acid cycle
P	0006102	biological_process	isocitrate metabolic process
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 PROSITE/UniProt

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

Chain	Residue	Details
D	ASN235-LEU254
B	ASN237-VAL256
C	ASN226-VAL245

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
B	LYS165
H	ASN94
H	ARG97
H	ARG128
H	ASP215
H	ASN273
H	THR274
H	ASN285
L	THR81
L	ASN94
L	ARG97
F	LYS165
L	ARG128
L	ASP215
L	ASN273
L	THR274
L	ASN285
P	THR81
P	ASN94
P	ARG97
P	ARG128
P	ASP215
J	LYS165
P	ASN273
P	THR274
P	ASN285
I	ARG119
I	ASP206
I	ASP230
I	ASP234
O	ARG88
O	ARG98
O	ARG119
N	LYS165
O	ASP206
O	ASP230
O	ASP234
M	ARG88
M	ARG98
M	ARG119
M	ASP206
M	ASP230
M	ASP234
D	ASP215
D	ASN273
D	THR274
D	ASN285
H	THR81

site_id	SWS_FT_FI2
Number of Residues	8
Details	SITE: Critical for catalysis => ECO:0000269\|PubMed:28098230, ECO:0000269\|PubMed:28139779

Chain	Residue	Details
C	TYR126
A	TYR126
G	TYR126
E	TYR126
K	TYR126
I	TYR126
O	TYR126
M	TYR126

site_id	SWS_FT_FI3
Number of Residues	8
Details	SITE: Critical for catalysis => ECO:0000269\|PubMed:28098230

Chain	Residue	Details
C	LYS173
A	LYS173
G	LYS173
E	LYS173
K	LYS173
I	LYS173
O	LYS173
M	LYS173

site_id	SWS_FT_FI4
Number of Residues	16
Details	MOD_RES: N6-succinyllysine => ECO:0000250\|UniProtKB:Q9D6R2

Chain	Residue	Details
C	LYS50
K	LYS323
I	LYS50
I	LYS323
O	LYS50
O	LYS323
M	LYS50
M	LYS323
C	LYS323
A	LYS50
A	LYS323
G	LYS50
G	LYS323
E	LYS50
E	LYS323
K	LYS50

site_id	SWS_FT_FI5
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:Q9D6R2

Chain	Residue	Details
C	THR74
A	THR74
G	THR74
E	THR74
K	THR74
I	THR74
O	THR74
M	THR74

site_id	SWS_FT_FI6
Number of Residues	8
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:Q9D6R2

Chain	Residue	Details
C	LYS196
A	LYS196
G	LYS196
E	LYS196
K	LYS196
I	LYS196
O	LYS196
M	LYS196

site_id	SWS_FT_FI7
Number of Residues	8
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:Q9D6R2

Chain	Residue	Details
C	LYS316
A	LYS316
G	LYS316
E	LYS316
K	LYS316
I	LYS316
O	LYS316
M	LYS316

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