Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3LCB

The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004674	molecular_function	protein serine/threonine kinase activity
A	0004721	molecular_function	phosphoprotein phosphatase activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0006006	biological_process	glucose metabolic process
A	0006097	biological_process	glyoxylate cycle
A	0006099	biological_process	tricarboxylic acid cycle
A	0008772	molecular_function	[isocitrate dehydrogenase (NADP+)] kinase activity
A	0016208	molecular_function	AMP binding
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0016787	molecular_function	hydrolase activity
A	0016788	molecular_function	hydrolase activity, acting on ester bonds
A	0016791	molecular_function	phosphatase activity
B	0000166	molecular_function	nucleotide binding
B	0004674	molecular_function	protein serine/threonine kinase activity
B	0004721	molecular_function	phosphoprotein phosphatase activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0006006	biological_process	glucose metabolic process
B	0006097	biological_process	glyoxylate cycle
B	0006099	biological_process	tricarboxylic acid cycle
B	0008772	molecular_function	[isocitrate dehydrogenase (NADP+)] kinase activity
B	0016208	molecular_function	AMP binding
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0016787	molecular_function	hydrolase activity
B	0016788	molecular_function	hydrolase activity, acting on ester bonds
B	0016791	molecular_function	phosphatase activity
C	0000287	molecular_function	magnesium ion binding
C	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006097	biological_process	glyoxylate cycle
C	0006099	biological_process	tricarboxylic acid cycle
C	0006979	biological_process	response to oxidative stress
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	0022900	biological_process	electron transport chain
C	0046872	molecular_function	metal ion binding
C	0051287	molecular_function	NAD binding
C	0097216	molecular_function	guanosine tetraphosphate binding
D	0000287	molecular_function	magnesium ion binding
D	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
D	0005515	molecular_function	protein binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006097	biological_process	glyoxylate cycle
D	0006099	biological_process	tricarboxylic acid cycle
D	0006979	biological_process	response to oxidative stress
D	0016491	molecular_function	oxidoreductase activity
D	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D	0022900	biological_process	electron transport chain
D	0046872	molecular_function	metal ion binding
D	0051287	molecular_function	NAD binding
D	0097216	molecular_function	guanosine tetraphosphate binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE AMP A 1604

Chain	Residue
A	ASN104
A	GLU376
A	ASN377
A	SER105
A	HIS113
A	LEU116
A	LYS291
A	LYS294
A	THR295
A	TYR298
A	PHE375

site_id	AC2
Number of Residues	22
Details	BINDING SITE FOR RESIDUE ATP A 1760

Chain	Residue
A	PRO316
A	GLY317
A	ILE318
A	GLY320
A	MET321
A	VAL322
A	MET323
A	VAL325
A	VAL334
A	LYS336
A	LYS346
A	GLU416
A	ARG417
A	MET419
A	PRO421
A	ASP457
A	LYS461
A	ASN462
A	TYR474
A	ASP475
A	ASP477
A	MG579

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 579

Chain	Residue
A	ASN462
A	ASP475
A	ATP1760

site_id	AC4
Number of Residues	20
Details	BINDING SITE FOR RESIDUE ATP B 1761

Chain	Residue
B	PRO316
B	ILE318
B	GLY320
B	MET321
B	VAL322
B	MET323
B	VAL325
B	VAL334
B	LYS336
B	LYS346
B	GLU416
B	ARG417
B	MET419
B	ASP457
B	LYS461
B	ASN462
B	TYR474
B	ASP475
B	ASP477
B	MG579

site_id	AC5
Number of Residues	11
Details	BINDING SITE FOR RESIDUE AMP B 1604

Chain	Residue
B	ASN104
B	SER105
B	HIS113
B	LEU116
B	LYS291
B	LYS294
B	THR295
B	TYR298
B	PHE375
B	GLU376
B	ASN377

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG B 579

Chain	Residue
B	ASN462
B	ASP475
B	ATP1761

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
C	ASN303-ILE322

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Active site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00747","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	14
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00747","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11284679","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2682654","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7761851","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1AI2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1HJ6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1IDE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10623532","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2204109","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1AI3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1CW1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1CW7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GRP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1P8F","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4BNP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5ICD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8ICD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10623532","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2204109","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1AI3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1CW7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GRP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1P8F","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4BNP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5ICD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8ICD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10623532","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1CW1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1CW4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11284679","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2682654","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7761851","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1AI2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1BL5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1HJ6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1IDE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ISO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9ICD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11284679","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2682654","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7761851","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1AI2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1BL5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1HJ6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1IDE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AJR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9ICD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11284679","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2682654","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7761851","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1AI2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9ICD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Site: {"description":"Critical for catalysis","evidences":[{"source":"PubMed","id":"7761851","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7819221","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"PubMed","id":"21151122","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"2204109","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"3112144","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	4
Details	M-CSA 7

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

site_id	MCSA2
Number of Residues	4
Details	M-CSA 7

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

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