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 | 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 | 0006470 | biological_process | protein dephosphorylation |
A | 0008772 | molecular_function | [isocitrate dehydrogenase (NADP+)] kinase activity |
A | 0016208 | molecular_function | AMP binding |
A | 0016310 | biological_process | phosphorylation |
A | 0016788 | molecular_function | hydrolase activity, acting on ester bonds |
A | 0016791 | molecular_function | phosphatase activity |
A | 0018105 | biological_process | peptidyl-serine phosphorylation |
A | 0050790 | biological_process | regulation of catalytic activity |
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 | 0006470 | biological_process | protein dephosphorylation |
B | 0008772 | molecular_function | [isocitrate dehydrogenase (NADP+)] kinase activity |
B | 0016208 | molecular_function | AMP binding |
B | 0016310 | biological_process | phosphorylation |
B | 0016788 | molecular_function | hydrolase activity, acting on ester bonds |
B | 0016791 | molecular_function | phosphatase activity |
B | 0018105 | biological_process | peptidyl-serine phosphorylation |
B | 0050790 | biological_process | regulation of catalytic 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 | 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 |
C | THR104 | |
D | THR104 |
site_id | SWS_FT_FI2 |
Number of Residues | 8 |
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 |
C | SER113 | |
C | ASN115 | |
C | ARG129 | |
C | ARG153 | |
D | SER113 | |
D | ASN115 | |
D | ARG129 | |
D | ARG153 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
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 |
C | ARG119 | |
D | ARG119 |
site_id | SWS_FT_FI4 |
Number of Residues | 2 |
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 |
C | ASP307 | |
D | ASP307 |
site_id | SWS_FT_FI5 |
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:1ISO, ECO:0007744|PDB:4AJ3, ECO:0007744|PDB:4AJR, ECO:0007744|PDB:9ICD |
Chain | Residue | Details |
C | HIS339 | |
D | HIS339 |
site_id | SWS_FT_FI6 |
Number of Residues | 4 |
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 |
C | ASN352 | |
C | TYR391 | |
D | ASN352 | |
D | TYR391 |
site_id | SWS_FT_FI7 |
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:9ICD |
Chain | Residue | Details |
C | ARG395 | |
D | ARG395 |
site_id | SWS_FT_FI8 |
Number of Residues | 4 |
Details | SITE: Critical for catalysis => ECO:0000269|PubMed:7761851, ECO:0000269|PubMed:7819221 |
Chain | Residue | Details |
C | TYR160 | |
C | LYS230 | |
D | TYR160 | |
D | LYS230 |
site_id | SWS_FT_FI9 |
Number of Residues | 4 |
Details | MOD_RES: N6-succinyllysine => ECO:0000269|PubMed:21151122 |
Chain | Residue | Details |
C | LYS100 | |
C | LYS242 | |
D | LYS100 | |
D | LYS242 |
site_id | SWS_FT_FI10 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:2204109, ECO:0000269|PubMed:3112144 |
Chain | Residue | Details |
C | SER113 | |
D | SER113 |
site_id | SWS_FT_FI11 |
Number of Residues | 2 |
Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:18723842 |
Chain | Residue | Details |
C | LYS142 | |
D | LYS142 |
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 |