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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4AJC

3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, calcium(II) and adenine nucleotide phosphate

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	16
Details	BINDING SITE FOR RESIDUE A2P A 501

Chain	Residue
A	ARG292
A	TYR391
A	ASP392
A	HOH2358
A	HOH2366
A	HOH2424
A	HOH2425
A	HOH2426
A	HIS339
A	GLY340
A	THR341
A	ALA342
A	LYS344
A	TYR345
A	VAL351
A	ASN352

site_id	AC2
Number of Residues	14
Details	BINDING SITE FOR RESIDUE AKG A 502

Chain	Residue
A	SER113
A	ASN115
A	ARG119
A	ARG129
A	ARG153
A	TYR160
A	LYS230
A	ASN232
A	ILE233
A	ASP307
A	CA503
A	HOH2168
A	HOH2287
A	HOH2428

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CA A 503

Chain	Residue
A	ASP283
A	ASP307
A	ASP311
A	AKG502
A	HOH2169
A	HOH2350
A	HOH2429

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	LYS235
A	HOH2138
A	HOH2143

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	MET100
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

219140

PDB entries from 2024-05-01

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