Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6KDY

Crystal structure of the alpha bata heterodimer of human IDH3 in complex with NAD.

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	0045242	cellular_component	isocitrate dehydrogenase complex (NAD+)
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	0045242	cellular_component	isocitrate dehydrogenase complex (NAD+)
C	0046872	molecular_function	metal ion binding
C	0051287	molecular_function	NAD binding
D	0000287	molecular_function	magnesium ion binding
D	0006099	biological_process	tricarboxylic acid cycle
D	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
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	0045242	cellular_component	isocitrate dehydrogenase complex (NAD+)
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	0045242	cellular_component	isocitrate dehydrogenase complex (NAD+)
G	0046872	molecular_function	metal ion binding
G	0051287	molecular_function	NAD binding
H	0000287	molecular_function	magnesium ion binding
H	0006099	biological_process	tricarboxylic acid cycle
H	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
H	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	18
Details	binding site for residue NAD A 401

Chain	Residue
A	ILE15
A	THR265
A	ALA266
A	ASP268
A	ILE269
A	ASN276
A	ASP317
B	ASN186
B	ILE215
B	ASN218
A	LYS69
A	PRO71
A	LEU72
A	THR74
A	ASN84
A	GLU260
A	HIS263
A	GLY264

site_id	AC2
Number of Residues	4
Details	binding site for residue PG4 B 401

Chain	Residue
B	HIS82
B	THR83
B	MET85
B	PRO276

site_id	AC3
Number of Residues	17
Details	binding site for residue NAD C 401

Chain	Residue
C	LYS69
C	PRO71
C	LEU72
C	THR74
C	ASN84
C	GLU260
C	SER261
C	HIS263
C	GLY264
C	THR265
C	ALA266
C	ASP268
C	ILE269
C	ASN276
D	ASN186
D	ILE215
D	ASN218

site_id	AC4
Number of Residues	6
Details	binding site for residue 2PE D 401

Chain	Residue
D	HIS82
D	THR83
D	PRO84
D	GLU90
D	PRO276
D	PG4402

site_id	AC5
Number of Residues	4
Details	binding site for residue PG4 D 402

Chain	Residue
D	ASP23
D	GLY24
D	GLN55
D	2PE401

site_id	AC6
Number of Residues	17
Details	binding site for residue NAD E 401

Chain	Residue
E	ILE15
E	LYS69
E	PRO71
E	LEU72
E	THR74
E	ASN84
E	GLU260
E	SER261
E	VAL262
E	HIS263
E	GLY264
E	THR265
E	ALA266
E	ILE269
E	ASN276
F	ILE215
F	ASN218

site_id	AC7
Number of Residues	4
Details	binding site for residue PE7 F 401

Chain	Residue
F	HIS82
F	THR83
F	MET85
F	PRO276

site_id	AC8
Number of Residues	16
Details	binding site for residue NAD G 401

Chain	Residue
G	ILE15
G	LYS69
G	PRO71
G	LEU72
G	THR74
G	ASN84
G	GLU260
G	HIS263
G	GLY264
G	THR265
G	ALA266
G	ASP268
G	ILE269
G	ASN276
H	ASN186
H	ASN218

site_id	AC9
Number of Residues	3
Details	binding site for residue P6G H 401

Chain	Residue
H	VAL54
H	HIS82
H	THR83

Functional Information from PROSITE/UniProt

site_id	PS00470
Number of Residues	20
Details	IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NLYGDIlSDlcAgli.GGLGV

Chain	Residue	Details
A	ASN226-VAL245
B	ASN237-VAL256

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
C	ASP206
C	ASP230
C	ASP234
E	ARG88
E	ARG98
E	ARG119
E	ASP206
E	ASP230
E	ASP234
G	ARG88
D	LYS165
G	ARG98
G	ARG119
G	ASP206
G	ASP230
G	ASP234
F	LYS165
H	LYS165
A	ASP230
A	ASP234
C	ARG88
C	ARG98
C	ARG119

site_id	SWS_FT_FI2
Number of Residues	4
Details	SITE: Critical for catalysis => ECO:0000269\|PubMed:28098230, ECO:0000269\|PubMed:28139779

Chain	Residue	Details
A	TYR126
C	TYR126
E	TYR126
G	TYR126

site_id	SWS_FT_FI3
Number of Residues	4
Details	SITE: Critical for catalysis => ECO:0000269\|PubMed:28098230

Chain	Residue	Details
A	LYS173
C	LYS173
E	LYS173
G	LYS173

site_id	SWS_FT_FI4
Number of Residues	8
Details	MOD_RES: N6-succinyllysine => ECO:0000250\|UniProtKB:Q9D6R2

Chain	Residue	Details
A	LYS50
A	LYS323
C	LYS50
C	LYS323
E	LYS50
E	LYS323
G	LYS50
G	LYS323

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:Q9D6R2

Chain	Residue	Details
A	THR74
C	THR74
E	THR74
G	THR74

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:Q9D6R2

Chain	Residue	Details
A	LYS196
C	LYS196
E	LYS196
G	LYS196

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:Q9D6R2

Chain	Residue	Details
A	LYS316
C	LYS316
E	LYS316
G	LYS316

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