1LWD
CRYSTAL STRUCTURE OF NADP-DEPENDENT ISOCITRATE DEHYDROGENASE FROM PORCINE HEART MITOCHONDRIA
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 | 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 |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0004450 | molecular_function | isocitrate dehydrogenase (NADP+) activity |
| B | 0005739 | cellular_component | mitochondrion |
| 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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN A 501 |
| Chain | Residue |
| A | ASP275 |
| A | ICT701 |
| A | HOH1001 |
| A | HOH1003 |
| B | ASP252 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN B 502 |
| Chain | Residue |
| A | ASP252 |
| B | ASP275 |
| B | ICT702 |
| B | HOH1002 |
| B | HOH1004 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 601 |
| Chain | Residue |
| B | HIS315 |
| B | LYS374 |
| B | HOH1565 |
| B | HOH1678 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 602 |
| Chain | Residue |
| A | LYS321 |
| A | ARG323 |
| B | ARG149 |
| site_id | AC5 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE ICT A 701 |
| Chain | Residue |
| A | THR78 |
| A | SER95 |
| A | ASN97 |
| A | ARG101 |
| A | ARG110 |
| A | ARG133 |
| A | TYR140 |
| A | ASP275 |
| A | MN501 |
| A | HOH1001 |
| A | HOH1003 |
| A | HOH1005 |
| A | HOH1283 |
| B | LYS212 |
| B | ASP252 |
| B | HOH1125 |
| site_id | AC6 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE ICT B 702 |
| Chain | Residue |
| A | LYS212 |
| A | ASP252 |
| B | THR78 |
| B | SER95 |
| B | ASN97 |
| B | ARG101 |
| B | ARG110 |
| B | ARG133 |
| B | TYR140 |
| B | ASP275 |
| B | MN502 |
| B | HOH1002 |
| B | HOH1004 |
| B | HOH1006 |
| B | HOH1187 |
| B | HOH1324 |
| site_id | MN1 |
| Number of Residues | 18 |
| Details | ACTIVE SITE OF ISOCITRATE DEHYDROGENASE IS WHERE OXIDATIVE DECARBOXYLATION OF ISOCITRATE TAKES PLACE. |
| Chain | Residue |
| A | ICT701 |
| A | SER278 |
| A | ASP279 |
| B | LYS212 |
| B | ASP252 |
| A | HOH1001 |
| A | HOH1003 |
| A | HOH1005 |
| B | HOH1007 |
| A | MN501 |
| A | THR78 |
| A | SER95 |
| A | ASN97 |
| A | ARG101 |
| A | ARG110 |
| A | ARG133 |
| A | TYR140 |
| A | ASP275 |
| site_id | MN2 |
| Number of Residues | 18 |
| Details | ACTIVE SITE OF ISOCITRATE DEHYDROGENASE IS WHERE OXIDATIVE DECARBOXYLATION OF ISOCITRATE TAKES PLACE. |
| Chain | Residue |
| B | ICT702 |
| B | THR78 |
| B | SER95 |
| B | ASN97 |
| B | ARG101 |
| B | ARG110 |
| B | ARG133 |
| B | TYR140 |
| B | ASP275 |
| B | SER278 |
| B | ASP279 |
| A | LYS212 |
| A | ASP252 |
| B | MN502 |
| B | HOH1002 |
| B | HOH1004 |
| B | HOH1006 |
| A | HOH1008 |
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 | ASN271-LEU290 |
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 | THR76 | |
| B | ASN328 | |
| A | ARG83 | |
| A | LYS260 | |
| A | GLY310 | |
| A | ASN328 | |
| B | THR76 | |
| B | ARG83 | |
| B | LYS260 | |
| B | GLY310 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12207025, ECO:0007744|PDB:1LWD |
| Chain | Residue | Details |
| A | THR78 | |
| B | ARG133 | |
| B | ASP252 | |
| B | ASP275 | |
| A | SER95 | |
| A | ARG110 | |
| A | ARG133 | |
| A | ASP252 | |
| A | ASP275 | |
| B | THR78 | |
| B | SER95 | |
| B | ARG110 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | SITE: Critical for catalysis => ECO:0000269|PubMed:14512428 |
| Chain | Residue | Details |
| A | TYR140 | |
| A | LYS212 | |
| B | TYR140 | |
| B | LYS212 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P54071 |
| Chain | Residue | Details |
| A | LYS6 | |
| B | LYS160 | |
| B | LYS241 | |
| B | LYS361 | |
| A | LYS9 | |
| A | LYS30 | |
| A | LYS160 | |
| A | LYS241 | |
| A | LYS361 | |
| B | LYS6 | |
| B | LYS9 | |
| B | LYS30 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 14 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P48735 |
| Chain | Residue | Details |
| A | LYS28 | |
| B | LYS224 | |
| B | LYS233 | |
| B | LYS236 | |
| B | LYS374 | |
| B | LYS403 | |
| A | LYS116 | |
| A | LYS224 | |
| A | LYS233 | |
| A | LYS236 | |
| A | LYS374 | |
| A | LYS403 | |
| B | LYS28 | |
| B | LYS116 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 16 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P54071 |
| Chain | Residue | Details |
| A | LYS41 | |
| B | LYS67 | |
| B | LYS127 | |
| B | LYS141 | |
| B | LYS154 | |
| B | LYS217 | |
| B | LYS243 | |
| B | LYS345 | |
| A | LYS67 | |
| A | LYS127 | |
| A | LYS141 | |
| A | LYS154 | |
| A | LYS217 | |
| A | LYS243 | |
| A | LYS345 | |
| B | LYS41 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1a05 |
| Chain | Residue | Details |
| A | LYS212 | |
| A | ASP252 | |
| B | VAL156 |
| site_id | CSA2 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1a05 |
| Chain | Residue | Details |
| A | VAL156 | |
| B | LYS212 | |
| B | ASP252 |
