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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4AJA

3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and thioNADP

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	30
Details	BINDING SITE FOR RESIDUE TAP A 501

Chain	Residue
A	LYS58
A	ALA342
A	TYR345
A	ASN352
A	TYR391
A	ASP392
A	ARG395
A	ICT502
A	HOH2169
A	HOH2424
A	HOH2425
A	LEU103
A	HOH2428
A	HOH2429
A	HOH2434
A	HOH2476
A	HOH2499
A	HOH2500
A	HOH2501
A	HOH2502
A	HOH2503
A	HOH2504
A	THR104
A	HOH2505
A	THR105
A	ASN115
A	ILE281
A	HIS339
A	GLY340
A	THR341

site_id	AC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ICT A 502

Chain	Residue
A	SER113
A	ASN115
A	ARG119
A	ARG129
A	ARG153
A	TYR160
A	LYS230
A	ASN232
A	ASP283
A	ASP307
A	TAP501
A	CA503
A	HOH2171
A	HOH2423
A	HOH2500

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 503

Chain	Residue
A	ASP283
A	ASP307
A	ASP311
A	ICT502
A	HOH2208
A	HOH2411

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 504

Chain	Residue
A	VAL107
A	GLY108
A	GLY109
A	GLY110
A	ILE111
A	LYS235
A	HOH2177

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 2024-07-10

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