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 | 0008772 | molecular_function | [isocitrate dehydrogenase (NADP+)] kinase activity |
| A | 0016788 | molecular_function | hydrolase activity, acting on ester bonds |
| A | 0016791 | molecular_function | phosphatase 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 | 0008772 | molecular_function | [isocitrate dehydrogenase (NADP+)] kinase 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 | 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 |
