6L59
Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with CIT, Mg and ATP binding at allosteric site and Mg, ATP binding at active site.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0004449 | molecular_function | isocitrate dehydrogenase (NAD+) activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005759 | cellular_component | mitochondrial matrix |
| A | 0005975 | biological_process | carbohydrate metabolic process |
| A | 0006099 | biological_process | tricarboxylic acid cycle |
| A | 0006102 | biological_process | isocitrate metabolic process |
| 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 | 0046872 | molecular_function | metal ion binding |
| A | 0051287 | molecular_function | NAD binding |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0004449 | molecular_function | isocitrate dehydrogenase (NAD+) activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005730 | cellular_component | nucleolus |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005759 | cellular_component | mitochondrial matrix |
| B | 0005975 | biological_process | carbohydrate metabolic process |
| B | 0006099 | biological_process | tricarboxylic acid cycle |
| B | 0006102 | biological_process | isocitrate metabolic process |
| B | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 12 |
| Details | binding site for residue ATP A 401 |
| Chain | Residue |
| A | ILE15 |
| A | HOH511 |
| B | HIS343 |
| B | ARG345 |
| A | HIS263 |
| A | GLY264 |
| A | THR265 |
| A | ALA266 |
| A | ASP268 |
| A | ASN276 |
| A | ASP317 |
| A | HOH506 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue MG A 402 |
| Chain | Residue |
| A | ASP230 |
| A | ASP234 |
| B | ASP215 |
| site_id | AC3 |
| Number of Residues | 18 |
| Details | binding site for residue ATP B 401 |
| Chain | Residue |
| B | ILE26 |
| B | PRO252 |
| B | ASN273 |
| B | THR274 |
| B | GLY275 |
| B | LYS276 |
| B | SER277 |
| B | ILE278 |
| B | ASN285 |
| B | ASP326 |
| B | HOH501 |
| B | HOH502 |
| B | HOH534 |
| B | HOH539 |
| B | HOH564 |
| B | HOH568 |
| B | HOH615 |
| B | HOH617 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 402 |
| Chain | Residue |
| A | HOH540 |
| B | ASN78 |
| B | ARG272 |
| B | CIT403 |
| B | HOH568 |
| B | HOH581 |
| site_id | AC5 |
| Number of Residues | 13 |
| Details | binding site for residue CIT B 403 |
| Chain | Residue |
| A | LYS173 |
| A | ASN175 |
| B | ASN78 |
| B | THR81 |
| B | SER91 |
| B | ASN93 |
| B | ARG97 |
| B | ARG128 |
| B | TYR135 |
| B | ASN239 |
| B | ARG272 |
| B | MG402 |
| B | HOH561 |
Functional Information from PROSITE/UniProt
| site_id | PS00470 |
| Number of Residues | 20 |
| Details | IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NLYGNIvNNvcAglv.GGPGL |
| Chain | Residue | Details |
| B | ASN235-LEU254 | |
| A | ASN226-VAL245 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:28098230 |
| Chain | Residue | Details |
| B | ARG128 | |
| B | ASP215 | |
| B | ASN273 | |
| B | THR274 | |
| B | ASN285 | |
| B | ASN94 | |
| B | ARG97 | |
| B | THR81 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | SITE: Critical for catalysis => ECO:0000269|PubMed:28098230, ECO:0000269|PubMed:28139779 |
| Chain | Residue | Details |
| A | TYR126 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | SITE: Critical for catalysis => ECO:0000269|PubMed:28098230 |
| Chain | Residue | Details |
| A | LYS173 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:Q9D6R2 |
| Chain | Residue | Details |
| A | LYS50 | |
| A | LYS323 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q9D6R2 |
| Chain | Residue | Details |
| A | THR74 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q9D6R2 |
| Chain | Residue | Details |
| A | LYS196 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q9D6R2 |
| Chain | Residue | Details |
| A | LYS316 |
