6VFZ
Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with NADPH and AG-881 (Vorasidenib) Inhibitor.
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 | 0005739 | cellular_component | mitochondrion |
| A | 0005759 | cellular_component | mitochondrial matrix |
| A | 0005777 | cellular_component | peroxisome |
| A | 0005829 | cellular_component | cytosol |
| A | 0005975 | biological_process | carbohydrate metabolic process |
| A | 0006097 | biological_process | glyoxylate cycle |
| A | 0006099 | biological_process | tricarboxylic acid cycle |
| A | 0006102 | biological_process | isocitrate metabolic process |
| A | 0006103 | biological_process | 2-oxoglutarate metabolic process |
| A | 0006739 | biological_process | NADP 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 |
| A | 0070062 | cellular_component | extracellular exosome |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0004450 | molecular_function | isocitrate dehydrogenase (NADP+) activity |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005759 | cellular_component | mitochondrial matrix |
| B | 0005777 | cellular_component | peroxisome |
| B | 0005829 | cellular_component | cytosol |
| B | 0005975 | biological_process | carbohydrate metabolic process |
| B | 0006097 | biological_process | glyoxylate cycle |
| B | 0006099 | biological_process | tricarboxylic acid cycle |
| B | 0006102 | biological_process | isocitrate metabolic process |
| B | 0006103 | biological_process | 2-oxoglutarate metabolic process |
| B | 0006739 | biological_process | NADP metabolic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| 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 |
| B | 0070062 | cellular_component | extracellular exosome |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 18 |
| Details | binding site for residue 9UO A 501 |
| Chain | Residue |
| A | TRP164 |
| B | TRP164 |
| B | VAL294 |
| B | VAL297 |
| B | LEU298 |
| B | ASP312 |
| B | VAL315 |
| B | GLN316 |
| B | ILE319 |
| B | LEU320 |
| A | VAL294 |
| A | VAL297 |
| A | LEU298 |
| A | ASP312 |
| A | VAL315 |
| A | GLN316 |
| A | ILE319 |
| A | LEU320 |
| site_id | AC2 |
| Number of Residues | 24 |
| Details | binding site for residue NDP A 502 |
| Chain | Residue |
| A | LYS112 |
| A | ALA114 |
| A | THR115 |
| A | ILE116 |
| A | THR117 |
| A | ARG122 |
| A | ASN136 |
| A | GLU345 |
| A | HIS348 |
| A | GLY349 |
| A | THR350 |
| A | VAL351 |
| A | THR352 |
| A | ARG353 |
| A | HIS354 |
| A | THR366 |
| A | ASN367 |
| A | HOH676 |
| A | HOH709 |
| A | HOH743 |
| A | HOH748 |
| A | HOH750 |
| A | HOH756 |
| A | HOH776 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue CA A 503 |
| Chain | Residue |
| A | ASP314 |
| A | ASP318 |
| A | HOH710 |
| A | HOH739 |
| A | HOH884 |
| B | ASP291 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue NA A 504 |
| Chain | Residue |
| A | ARG149 |
| A | ILE170 |
| A | SER317 |
| A | HOH924 |
| site_id | AC5 |
| Number of Residues | 21 |
| Details | binding site for residue NDP B 501 |
| Chain | Residue |
| B | LYS112 |
| B | THR115 |
| B | ILE116 |
| B | THR117 |
| B | ARG122 |
| B | ASN136 |
| B | GLU345 |
| B | HIS348 |
| B | GLY349 |
| B | THR350 |
| B | VAL351 |
| B | THR352 |
| B | ARG353 |
| B | HIS354 |
| B | THR366 |
| B | ASN367 |
| B | HOH650 |
| B | HOH668 |
| B | HOH725 |
| B | HOH733 |
| B | HOH777 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue CA B 502 |
| Chain | Residue |
| A | ASP291 |
| B | ASP314 |
| B | ASP318 |
| B | HOH696 |
| B | HOH772 |
| B | HOH778 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue NA B 503 |
| Chain | Residue |
| B | ARG149 |
| B | ILE170 |
| B | SER317 |
| B | HOH830 |
Functional Information from PROSITE/UniProt
| site_id | PS00470 |
| Number of Residues | 20 |
| Details | IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NYDGDVqSDilAqgf.GSLGL |
| Chain | Residue | Details |
| A | ASN310-LEU329 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 10 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:O75874 |
| Chain | Residue | Details |
| A | THR115 | |
| B | ASN367 | |
| A | ARG122 | |
| A | LYS299 | |
| A | GLY349 | |
| A | ASN367 | |
| B | THR115 | |
| B | ARG122 | |
| B | LYS299 | |
| B | GLY349 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P33198 |
| Chain | Residue | Details |
| A | THR117 | |
| B | ARG172 | |
| B | ASP291 | |
| B | ASP314 | |
| A | SER134 | |
| A | ARG149 | |
| A | ARG172 | |
| A | ASP291 | |
| A | ASP314 | |
| B | THR117 | |
| B | SER134 | |
| B | ARG149 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | SITE: Critical for catalysis => ECO:0000250|UniProtKB:P33198 |
| Chain | Residue | Details |
| A | TYR179 | |
| A | LYS251 | |
| B | TYR179 | |
| B | LYS251 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P54071 |
| Chain | Residue | Details |
| A | LYS45 | |
| B | LYS199 | |
| B | LYS280 | |
| B | LYS400 | |
| A | LYS48 | |
| A | LYS69 | |
| A | LYS199 | |
| A | LYS280 | |
| A | LYS400 | |
| B | LYS45 | |
| B | LYS48 | |
| B | LYS69 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS67 | |
| B | LYS272 | |
| B | LYS275 | |
| B | LYS442 | |
| A | LYS155 | |
| A | LYS263 | |
| A | LYS272 | |
| A | LYS275 | |
| A | LYS442 | |
| B | LYS67 | |
| B | LYS155 | |
| B | LYS263 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 16 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P54071 |
| Chain | Residue | Details |
| A | LYS80 | |
| B | LYS106 | |
| B | LYS166 | |
| B | LYS180 | |
| B | LYS193 | |
| B | LYS256 | |
| B | LYS282 | |
| B | LYS384 | |
| A | LYS106 | |
| A | LYS166 | |
| A | LYS180 | |
| A | LYS193 | |
| A | LYS256 | |
| A | LYS282 | |
| A | LYS384 | |
| B | LYS80 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:22416140 |
| Chain | Residue | Details |
| A | LYS413 | |
| B | LYS413 |
