2QFX
Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with NADPH, a-ketoglutarate and Ca(2+)
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 | 0005515 | molecular_function | protein binding |
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 | 0006537 | biological_process | glutamate biosynthetic 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 | 0042645 | cellular_component | mitochondrial nucleoid |
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 | 0005515 | molecular_function | protein binding |
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 | 0006537 | biological_process | glutamate biosynthetic 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 | 0042645 | cellular_component | mitochondrial nucleoid |
B | 0046872 | molecular_function | metal ion binding |
B | 0051287 | molecular_function | NAD binding |
C | 0000287 | molecular_function | magnesium ion binding |
C | 0004450 | molecular_function | isocitrate dehydrogenase (NADP+) activity |
C | 0005515 | molecular_function | protein binding |
C | 0005739 | cellular_component | mitochondrion |
C | 0006097 | biological_process | glyoxylate cycle |
C | 0006099 | biological_process | tricarboxylic acid cycle |
C | 0006102 | biological_process | isocitrate metabolic process |
C | 0006537 | biological_process | glutamate biosynthetic process |
C | 0006739 | biological_process | NADP metabolic process |
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 | 0042645 | cellular_component | mitochondrial nucleoid |
C | 0046872 | molecular_function | metal ion binding |
C | 0051287 | molecular_function | NAD binding |
D | 0000287 | molecular_function | magnesium ion binding |
D | 0004450 | molecular_function | isocitrate dehydrogenase (NADP+) activity |
D | 0005515 | molecular_function | protein binding |
D | 0005739 | cellular_component | mitochondrion |
D | 0006097 | biological_process | glyoxylate cycle |
D | 0006099 | biological_process | tricarboxylic acid cycle |
D | 0006102 | biological_process | isocitrate metabolic process |
D | 0006537 | biological_process | glutamate biosynthetic process |
D | 0006739 | biological_process | NADP metabolic process |
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 | 0042645 | cellular_component | mitochondrial nucleoid |
D | 0046872 | molecular_function | metal ion binding |
D | 0051287 | molecular_function | NAD binding |
E | 0000287 | molecular_function | magnesium ion binding |
E | 0004450 | molecular_function | isocitrate dehydrogenase (NADP+) activity |
E | 0005515 | molecular_function | protein binding |
E | 0005739 | cellular_component | mitochondrion |
E | 0006097 | biological_process | glyoxylate cycle |
E | 0006099 | biological_process | tricarboxylic acid cycle |
E | 0006102 | biological_process | isocitrate metabolic process |
E | 0006537 | biological_process | glutamate biosynthetic process |
E | 0006739 | biological_process | NADP metabolic process |
E | 0016491 | molecular_function | oxidoreductase activity |
E | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
E | 0042645 | cellular_component | mitochondrial nucleoid |
E | 0046872 | molecular_function | metal ion binding |
E | 0051287 | molecular_function | NAD binding |
F | 0000287 | molecular_function | magnesium ion binding |
F | 0004450 | molecular_function | isocitrate dehydrogenase (NADP+) activity |
F | 0005515 | molecular_function | protein binding |
F | 0005739 | cellular_component | mitochondrion |
F | 0006097 | biological_process | glyoxylate cycle |
F | 0006099 | biological_process | tricarboxylic acid cycle |
F | 0006102 | biological_process | isocitrate metabolic process |
F | 0006537 | biological_process | glutamate biosynthetic process |
F | 0006739 | biological_process | NADP metabolic process |
F | 0016491 | molecular_function | oxidoreductase activity |
F | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
F | 0042645 | cellular_component | mitochondrial nucleoid |
F | 0046872 | molecular_function | metal ion binding |
F | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CA A 1103 |
Chain | Residue |
A | ASP277 |
A | ASP281 |
B | ASP254 |
site_id | AC2 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CA B 1203 |
Chain | Residue |
A | ASP254 |
B | ASP277 |
B | ASP281 |
site_id | AC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CA C 1303 |
Chain | Residue |
C | HOH1306 |
D | ASP254 |
C | ARG110 |
C | ASP277 |
C | ASP281 |
site_id | AC4 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CA D 1403 |
Chain | Residue |
C | ASP254 |
D | ASP277 |
D | ASP281 |
site_id | AC5 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CA E 1503 |
Chain | Residue |
E | ASP277 |
E | ASP281 |
F | ASP254 |
site_id | AC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CA F 1603 |
Chain | Residue |
E | ASP254 |
F | ASP277 |
F | ASP281 |
site_id | AC7 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE NDP A 1101 |
Chain | Residue |
A | LYS73 |
A | ALA75 |
A | THR76 |
A | ILE77 |
A | THR78 |
A | ARG83 |
A | ASN97 |
A | LEU290 |
A | HIS311 |
A | GLY312 |
A | THR313 |
A | THR315 |
A | ARG316 |
A | HIS317 |
A | ASN330 |
A | HOH1106 |
A | HOH1113 |
A | HOH1116 |
A | HOH1120 |
B | ASP255 |
B | GLN259 |
B | LYS262 |
site_id | AC8 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE AKG A 1102 |
Chain | Residue |
A | THR78 |
A | SER95 |
A | ASN97 |
A | ARG101 |
A | ARG110 |
A | ASP277 |
A | ALA310 |
A | HOH1120 |
A | HOH1123 |
B | ASP254 |
site_id | AC9 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE NDP B 1201 |
Chain | Residue |
A | GLN259 |
A | LYS262 |
B | LYS73 |
B | ALA75 |
B | THR76 |
B | ILE77 |
B | THR78 |
B | ARG83 |
B | ASN97 |
B | LEU290 |
B | HIS311 |
B | GLY312 |
B | THR313 |
B | THR315 |
B | ARG316 |
B | HIS317 |
B | ASN330 |
site_id | BC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE AKG B 1202 |
Chain | Residue |
A | LYS214 |
A | ASP254 |
B | THR78 |
B | SER95 |
B | ASN97 |
B | ARG101 |
B | ARG110 |
B | ALA310 |
site_id | BC2 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE NDP C 1301 |
Chain | Residue |
C | LYS73 |
C | ALA75 |
C | THR76 |
C | ILE77 |
C | THR78 |
C | ARG83 |
C | ASN97 |
C | LEU290 |
C | HIS311 |
C | GLY312 |
C | THR313 |
C | THR315 |
C | ARG316 |
C | HIS317 |
C | THR329 |
C | ASN330 |
C | HOH1308 |
C | HOH1319 |
C | HOH1329 |
D | LEU252 |
D | GLN259 |
D | LYS262 |
site_id | BC3 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE AKG C 1302 |
Chain | Residue |
C | THR78 |
C | SER95 |
C | ASN97 |
C | ARG101 |
C | ARG110 |
C | ARG133 |
C | ALA310 |
C | HOH1306 |
C | HOH1329 |
D | ASP254 |
site_id | BC4 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE NDP D 1401 |
Chain | Residue |
C | ASP255 |
C | GLN259 |
C | LYS262 |
C | HOH1311 |
D | LYS73 |
D | ALA75 |
D | THR76 |
D | ILE77 |
D | THR78 |
D | ARG83 |
D | ASN97 |
D | LEU290 |
D | GLU308 |
D | HIS311 |
D | GLY312 |
D | THR313 |
D | THR315 |
D | ARG316 |
D | HIS317 |
D | ASN330 |
D | HOH1415 |
site_id | BC5 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE AKG D 1402 |
Chain | Residue |
C | ASP254 |
D | THR78 |
D | SER95 |
D | ASN97 |
D | ARG101 |
D | ARG110 |
D | ARG133 |
D | ASP277 |
site_id | BC6 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE NDP E 1501 |
Chain | Residue |
E | LYS73 |
E | ALA75 |
E | THR76 |
E | ILE77 |
E | THR78 |
E | ARG83 |
E | ASN97 |
E | LEU290 |
E | HIS311 |
E | GLY312 |
E | THR313 |
E | THR315 |
E | ARG316 |
E | HIS317 |
E | ASN330 |
E | HOH1506 |
E | HOH1513 |
F | LEU252 |
F | ASP255 |
F | GLN259 |
F | LYS262 |
F | HOH1612 |
site_id | BC7 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE AKG E 1502 |
Chain | Residue |
E | THR78 |
E | SER95 |
E | ARG101 |
E | ARG110 |
E | ARG133 |
E | ASP277 |
F | ASP254 |
site_id | BC8 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE NDP F 1601 |
Chain | Residue |
E | ASP255 |
E | GLN259 |
E | LYS262 |
F | LYS73 |
F | ALA75 |
F | THR76 |
F | ILE77 |
F | THR78 |
F | ARG83 |
F | ASN97 |
F | LEU290 |
F | HIS311 |
F | GLY312 |
F | THR313 |
F | THR315 |
F | ARG316 |
F | HIS317 |
F | ASN330 |
F | HOH1609 |
site_id | BC9 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE AKG F 1602 |
Chain | Residue |
E | ASP254 |
F | THR78 |
F | SER95 |
F | ASN97 |
F | ARG101 |
F | ARG110 |
F | ARG133 |
F | ASP277 |
F | HOH1618 |
Functional Information from PROSITE/UniProt
site_id | PS00470 |
Number of Residues | 20 |
Details | IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NYDGDVqSDivAqgf.GSLGL |
Chain | Residue | Details |
A | ASN273-LEU292 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 66 |
Details | BINDING: BINDING => ECO:0000250 |
Chain | Residue | Details |
A | THR76 | |
A | GLY312 | |
A | ASN330 | |
B | THR76 | |
B | THR78 | |
B | ARG83 | |
B | SER95 | |
B | ARG110 | |
B | ARG133 | |
B | ASP254 | |
B | LYS262 | |
A | THR78 | |
B | ASP277 | |
B | GLY312 | |
B | ASN330 | |
C | THR76 | |
C | THR78 | |
C | ARG83 | |
C | SER95 | |
C | ARG110 | |
C | ARG133 | |
C | ASP254 | |
A | ARG83 | |
C | LYS262 | |
C | ASP277 | |
C | GLY312 | |
C | ASN330 | |
D | THR76 | |
D | THR78 | |
D | ARG83 | |
D | SER95 | |
D | ARG110 | |
D | ARG133 | |
A | SER95 | |
D | ASP254 | |
D | LYS262 | |
D | ASP277 | |
D | GLY312 | |
D | ASN330 | |
E | THR76 | |
E | THR78 | |
E | ARG83 | |
E | SER95 | |
E | ARG110 | |
A | ARG110 | |
E | ARG133 | |
E | ASP254 | |
E | LYS262 | |
E | ASP277 | |
E | GLY312 | |
E | ASN330 | |
F | THR76 | |
F | THR78 | |
F | ARG83 | |
F | SER95 | |
A | ARG133 | |
F | ARG110 | |
F | ARG133 | |
F | ASP254 | |
F | LYS262 | |
F | ASP277 | |
F | GLY312 | |
F | ASN330 | |
A | ASP254 | |
A | LYS262 | |
A | ASP277 |
site_id | SWS_FT_FI2 |
Number of Residues | 12 |
Details | SITE: Critical for catalysis => ECO:0000250 |
Chain | Residue | Details |
A | TYR140 | |
E | LYS214 | |
F | TYR140 | |
F | LYS214 | |
A | LYS214 | |
B | TYR140 | |
B | LYS214 | |
C | TYR140 | |
C | LYS214 | |
D | TYR140 | |
D | LYS214 | |
E | TYR140 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
A | VAL156 |
site_id | CSA10 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
D | ASP254 | |
D | LYS214 |
site_id | CSA11 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
E | ASP254 | |
E | LYS214 |
site_id | CSA12 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
F | ASP254 | |
F | LYS214 |
site_id | CSA13 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
A | THR163 |
site_id | CSA14 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
B | THR163 |
site_id | CSA15 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
C | THR163 |
site_id | CSA16 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
D | THR163 |
site_id | CSA17 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
E | THR163 |
site_id | CSA18 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
F | THR163 |
site_id | CSA2 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
B | VAL156 |
site_id | CSA3 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
C | VAL156 |
site_id | CSA4 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
D | VAL156 |
site_id | CSA5 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
E | VAL156 |
site_id | CSA6 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
F | VAL156 |
site_id | CSA7 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
A | ASP254 | |
A | LYS214 |
site_id | CSA8 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
B | ASP254 | |
B | LYS214 |
site_id | CSA9 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
C | ASP254 | |
C | LYS214 |