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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4AJ3

3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and NADP - The pseudo-Michaelis complex

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	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006097	biological_process	glyoxylate cycle
A	0006099	biological_process	tricarboxylic acid cycle
A	0006979	biological_process	response to oxidative stress
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	0022900	biological_process	electron transport chain
A	0046872	molecular_function	metal ion binding
A	0051287	molecular_function	NAD binding
A	0097216	molecular_function	guanosine tetraphosphate binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	34
Details	BINDING SITE FOR RESIDUE NAP A 1417

Chain	Residue
A	ILE37
A	ALA284
A	GLN288
A	ARG292
A	ILE320
A	GLU336
A	THR338
A	HIS339
A	GLY340
A	THR341
A	ALA342
A	LYS100
A	TYR345
A	VAL351
A	ASN352
A	TYR391
A	ASP392
A	ICT1418
A	HOH2288
A	HOH2291
A	HOH2299
A	HOH2311
A	PRO102
A	HOH2370
A	HOH2371
A	HOH2372
A	HOH2373
A	HOH2374
A	LEU103
A	THR104
A	THR105
A	ASN115
A	ASN232
A	ILE281

site_id	AC2
Number of Residues	14
Details	BINDING SITE FOR RESIDUE ICT A 1418

Chain	Residue
A	THR105
A	SER113
A	ASN115
A	ARG119
A	ARG129
A	ARG153
A	TYR160
A	LYS230
A	ILE233
A	ASP283
A	ASP307
A	NAP1417
A	CA1419
A	HOH2258

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 1419

Chain	Residue
A	ASP283
A	ASP307
A	ASP311
A	ICT1418
A	HOH2156
A	HOH2298

Functional Information from PROSITE/UniProt

site_id	PS00470
Number of Residues	20
Details	IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NLNGDYiSDalAaqv.GGIGI

Chain	Residue	Details
A	ASN303-ILE322

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:11284679, ECO:0000269\|PubMed:2682654, ECO:0000269\|PubMed:7761851, ECO:0007744\|PDB:1AI2, ECO:0007744\|PDB:1HJ6, ECO:0007744\|PDB:1IDE, ECO:0007744\|PDB:4AJ3, ECO:0007744\|PDB:4AJR

Chain	Residue	Details
A	THR104

site_id	SWS_FT_FI2
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:10623532, ECO:0000269\|PubMed:2204109, ECO:0007744\|PDB:1AI3, ECO:0007744\|PDB:1CW1, ECO:0007744\|PDB:1CW7, ECO:0007744\|PDB:1GRP, ECO:0007744\|PDB:1P8F, ECO:0007744\|PDB:1PB1, ECO:0007744\|PDB:4AJ3, ECO:0007744\|PDB:4AJA, ECO:0007744\|PDB:4AJB, ECO:0007744\|PDB:4AJS, ECO:0007744\|PDB:4BNP, ECO:0007744\|PDB:5ICD, ECO:0007744\|PDB:8ICD

Chain	Residue	Details
A	SER113
A	ASN115
A	ARG129
A	ARG153

site_id	SWS_FT_FI3
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:10623532, ECO:0000269\|PubMed:2204109, ECO:0007744\|PDB:1AI3, ECO:0007744\|PDB:1CW7, ECO:0007744\|PDB:1GRP, ECO:0007744\|PDB:1P8F, ECO:0007744\|PDB:1PB1, ECO:0007744\|PDB:4AJ3, ECO:0007744\|PDB:4AJA, ECO:0007744\|PDB:4AJB, ECO:0007744\|PDB:4AJS, ECO:0007744\|PDB:4BNP, ECO:0007744\|PDB:5ICD, ECO:0007744\|PDB:8ICD

Chain	Residue	Details
A	ARG119

site_id	SWS_FT_FI4
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:11284679, ECO:0000269\|PubMed:2204109, ECO:0000269\|PubMed:7761851, ECO:0007744\|PDB:1AI3, ECO:0007744\|PDB:1BL5, ECO:0007744\|PDB:1GRP, ECO:0007744\|PDB:1HJ6, ECO:0007744\|PDB:1IDC, ECO:0007744\|PDB:1P8F, ECO:0007744\|PDB:4AJB, ECO:0007744\|PDB:4AJR, ECO:0007744\|PDB:4AJS, ECO:0007744\|PDB:4BNP, ECO:0007744\|PDB:8ICD

Chain	Residue	Details
A	ASP307

site_id	SWS_FT_FI5
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:11284679, ECO:0000269\|PubMed:2682654, ECO:0000269\|PubMed:7761851, ECO:0007744\|PDB:1AI2, ECO:0007744\|PDB:1BL5, ECO:0007744\|PDB:1HJ6, ECO:0007744\|PDB:1IDE, ECO:0007744\|PDB:1ISO, ECO:0007744\|PDB:4AJ3, ECO:0007744\|PDB:4AJR, ECO:0007744\|PDB:9ICD

Chain	Residue	Details
A	HIS339

site_id	SWS_FT_FI6
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269\|PubMed:11284679, ECO:0000269\|PubMed:2682654, ECO:0000269\|PubMed:7761851, ECO:0007744\|PDB:1AI2, ECO:0007744\|PDB:1BL5, ECO:0007744\|PDB:1HJ6, ECO:0007744\|PDB:1IDE, ECO:0007744\|PDB:4AJ3, ECO:0007744\|PDB:4AJR, ECO:0007744\|PDB:9ICD

Chain	Residue	Details
A	ASN352
A	TYR391

site_id	SWS_FT_FI7
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:11284679, ECO:0000269\|PubMed:2682654, ECO:0000269\|PubMed:7761851, ECO:0007744\|PDB:1AI2, ECO:0007744\|PDB:9ICD

Chain	Residue	Details
A	ARG395

site_id	SWS_FT_FI8
Number of Residues	2
Details	SITE: Critical for catalysis => ECO:0000269\|PubMed:7761851, ECO:0000269\|PubMed:7819221

Chain	Residue	Details
A	TYR160
A	LYS230

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: N6-succinyllysine => ECO:0000269\|PubMed:21151122

Chain	Residue	Details
A	LYS100
A	LYS242

site_id	SWS_FT_FI10
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000269\|PubMed:2204109, ECO:0000269\|PubMed:3112144

Chain	Residue	Details
A	SER113

site_id	SWS_FT_FI11
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:18723842

Chain	Residue	Details
A	LYS142

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	4
Details	M-CSA 7

Chain	Residue	Details
A	TYR160	electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
A	LYS230	electrostatic stabiliser, proton acceptor, proton donor, proton relay
A	ASP283	electrostatic stabiliser, proton acceptor, proton donor
A	ASP307	metal ligand

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PDB entries from 2024-06-26

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