1T0L
Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP, isocitrate, and calcium(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 | 0005576 | cellular_component | extracellular region |
A | 0005737 | cellular_component | cytoplasm |
A | 0005739 | cellular_component | mitochondrion |
A | 0005777 | cellular_component | peroxisome |
A | 0005782 | cellular_component | peroxisomal matrix |
A | 0005829 | cellular_component | cytosol |
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 | 0006749 | biological_process | glutathione metabolic process |
A | 0006979 | biological_process | response to oxidative stress |
A | 0008585 | biological_process | female gonad development |
A | 0014070 | biological_process | response to organic cyclic compound |
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 | 0034774 | cellular_component | secretory granule lumen |
A | 0042802 | molecular_function | identical protein binding |
A | 0042803 | molecular_function | protein homodimerization activity |
A | 0045296 | molecular_function | cadherin binding |
A | 0046872 | molecular_function | metal ion binding |
A | 0048545 | biological_process | response to steroid hormone |
A | 0050661 | molecular_function | NADP binding |
A | 0051287 | molecular_function | NAD binding |
A | 0060696 | biological_process | regulation of phospholipid catabolic process |
A | 0070062 | cellular_component | extracellular exosome |
A | 0071071 | biological_process | regulation of phospholipid biosynthetic process |
A | 1904724 | cellular_component | tertiary granule lumen |
A | 1904813 | cellular_component | ficolin-1-rich granule lumen |
B | 0000287 | molecular_function | magnesium ion binding |
B | 0004450 | molecular_function | isocitrate dehydrogenase (NADP+) activity |
B | 0005515 | molecular_function | protein binding |
B | 0005576 | cellular_component | extracellular region |
B | 0005737 | cellular_component | cytoplasm |
B | 0005739 | cellular_component | mitochondrion |
B | 0005777 | cellular_component | peroxisome |
B | 0005782 | cellular_component | peroxisomal matrix |
B | 0005829 | cellular_component | cytosol |
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 | 0006749 | biological_process | glutathione metabolic process |
B | 0006979 | biological_process | response to oxidative stress |
B | 0008585 | biological_process | female gonad development |
B | 0014070 | biological_process | response to organic cyclic compound |
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 | 0034774 | cellular_component | secretory granule lumen |
B | 0042802 | molecular_function | identical protein binding |
B | 0042803 | molecular_function | protein homodimerization activity |
B | 0045296 | molecular_function | cadherin binding |
B | 0046872 | molecular_function | metal ion binding |
B | 0048545 | biological_process | response to steroid hormone |
B | 0050661 | molecular_function | NADP binding |
B | 0051287 | molecular_function | NAD binding |
B | 0060696 | biological_process | regulation of phospholipid catabolic process |
B | 0070062 | cellular_component | extracellular exosome |
B | 0071071 | biological_process | regulation of phospholipid biosynthetic process |
B | 1904724 | cellular_component | tertiary granule lumen |
B | 1904813 | cellular_component | ficolin-1-rich granule lumen |
C | 0000287 | molecular_function | magnesium ion binding |
C | 0004450 | molecular_function | isocitrate dehydrogenase (NADP+) activity |
C | 0005515 | molecular_function | protein binding |
C | 0005576 | cellular_component | extracellular region |
C | 0005737 | cellular_component | cytoplasm |
C | 0005739 | cellular_component | mitochondrion |
C | 0005777 | cellular_component | peroxisome |
C | 0005782 | cellular_component | peroxisomal matrix |
C | 0005829 | cellular_component | cytosol |
C | 0006097 | biological_process | glyoxylate cycle |
C | 0006099 | biological_process | tricarboxylic acid cycle |
C | 0006102 | biological_process | isocitrate metabolic process |
C | 0006103 | biological_process | 2-oxoglutarate metabolic process |
C | 0006739 | biological_process | NADP metabolic process |
C | 0006749 | biological_process | glutathione metabolic process |
C | 0006979 | biological_process | response to oxidative stress |
C | 0008585 | biological_process | female gonad development |
C | 0014070 | biological_process | response to organic cyclic compound |
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 | 0034774 | cellular_component | secretory granule lumen |
C | 0042802 | molecular_function | identical protein binding |
C | 0042803 | molecular_function | protein homodimerization activity |
C | 0045296 | molecular_function | cadherin binding |
C | 0046872 | molecular_function | metal ion binding |
C | 0048545 | biological_process | response to steroid hormone |
C | 0050661 | molecular_function | NADP binding |
C | 0051287 | molecular_function | NAD binding |
C | 0060696 | biological_process | regulation of phospholipid catabolic process |
C | 0070062 | cellular_component | extracellular exosome |
C | 0071071 | biological_process | regulation of phospholipid biosynthetic process |
C | 1904724 | cellular_component | tertiary granule lumen |
C | 1904813 | cellular_component | ficolin-1-rich granule lumen |
D | 0000287 | molecular_function | magnesium ion binding |
D | 0004450 | molecular_function | isocitrate dehydrogenase (NADP+) activity |
D | 0005515 | molecular_function | protein binding |
D | 0005576 | cellular_component | extracellular region |
D | 0005737 | cellular_component | cytoplasm |
D | 0005739 | cellular_component | mitochondrion |
D | 0005777 | cellular_component | peroxisome |
D | 0005782 | cellular_component | peroxisomal matrix |
D | 0005829 | cellular_component | cytosol |
D | 0006097 | biological_process | glyoxylate cycle |
D | 0006099 | biological_process | tricarboxylic acid cycle |
D | 0006102 | biological_process | isocitrate metabolic process |
D | 0006103 | biological_process | 2-oxoglutarate metabolic process |
D | 0006739 | biological_process | NADP metabolic process |
D | 0006749 | biological_process | glutathione metabolic process |
D | 0006979 | biological_process | response to oxidative stress |
D | 0008585 | biological_process | female gonad development |
D | 0014070 | biological_process | response to organic cyclic compound |
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 | 0034774 | cellular_component | secretory granule lumen |
D | 0042802 | molecular_function | identical protein binding |
D | 0042803 | molecular_function | protein homodimerization activity |
D | 0045296 | molecular_function | cadherin binding |
D | 0046872 | molecular_function | metal ion binding |
D | 0048545 | biological_process | response to steroid hormone |
D | 0050661 | molecular_function | NADP binding |
D | 0051287 | molecular_function | NAD binding |
D | 0060696 | biological_process | regulation of phospholipid catabolic process |
D | 0070062 | cellular_component | extracellular exosome |
D | 0071071 | biological_process | regulation of phospholipid biosynthetic process |
D | 1904724 | cellular_component | tertiary granule lumen |
D | 1904813 | cellular_component | ficolin-1-rich granule lumen |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA A 1717 |
Chain | Residue |
A | ARG109 |
A | ASP275 |
A | ASP279 |
A | ICT1616 |
A | HOH1763 |
B | ASP252 |
site_id | AC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CA B 1718 |
Chain | Residue |
B | ICT1617 |
B | HOH1897 |
A | ASP252 |
B | ASP275 |
B | ASP279 |
site_id | AC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA C 1719 |
Chain | Residue |
C | ASP275 |
C | ASP279 |
C | ICT1618 |
C | HOH1733 |
C | HOH1859 |
D | ASP252 |
site_id | AC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA D 1720 |
Chain | Residue |
C | ASP252 |
D | ASP275 |
D | ASP279 |
D | ICT1619 |
D | HOH1806 |
D | HOH1815 |
site_id | AC5 |
Number of Residues | 31 |
Details | BINDING SITE FOR RESIDUE NAP A 1515 |
Chain | Residue |
A | LYS72 |
A | ALA74 |
A | THR75 |
A | ILE76 |
A | THR77 |
A | ARG82 |
A | ASN96 |
A | LEU288 |
A | ALA308 |
A | HIS309 |
A | GLY310 |
A | THR311 |
A | VAL312 |
A | THR313 |
A | ARG314 |
A | HIS315 |
A | THR327 |
A | ASN328 |
A | ICT1616 |
A | HOH1718 |
A | HOH1720 |
A | HOH1773 |
A | HOH1782 |
A | HOH1807 |
A | HOH1844 |
A | HOH1856 |
A | HOH1859 |
A | HOH1914 |
B | GLN257 |
B | LYS260 |
B | HOH1799 |
site_id | AC6 |
Number of Residues | 29 |
Details | BINDING SITE FOR RESIDUE NAP B 1516 |
Chain | Residue |
A | ASP253 |
A | GLN257 |
A | LYS260 |
B | LYS72 |
B | ALA74 |
B | THR75 |
B | ILE76 |
B | THR77 |
B | ARG82 |
B | ASN96 |
B | LEU288 |
B | ALA308 |
B | HIS309 |
B | GLY310 |
B | THR311 |
B | VAL312 |
B | THR313 |
B | ARG314 |
B | HIS315 |
B | ASN328 |
B | ICT1617 |
B | HOH1721 |
B | HOH1722 |
B | HOH1737 |
B | HOH1741 |
B | HOH1749 |
B | HOH1803 |
B | HOH1872 |
B | HOH1897 |
site_id | AC7 |
Number of Residues | 31 |
Details | BINDING SITE FOR RESIDUE NAP C 1517 |
Chain | Residue |
C | THR327 |
C | ASN328 |
C | ICT1618 |
C | HOH1723 |
C | HOH1727 |
C | HOH1739 |
C | HOH1743 |
C | HOH1746 |
C | HOH1793 |
C | HOH1819 |
C | HOH1852 |
C | HOH1907 |
D | ASP253 |
D | GLN257 |
D | LYS260 |
C | LYS72 |
C | ALA74 |
C | THR75 |
C | ILE76 |
C | THR77 |
C | ARG82 |
C | ASN96 |
C | LEU288 |
C | ALA308 |
C | HIS309 |
C | GLY310 |
C | THR311 |
C | VAL312 |
C | THR313 |
C | ARG314 |
C | HIS315 |
site_id | AC8 |
Number of Residues | 27 |
Details | BINDING SITE FOR RESIDUE NAP D 1518 |
Chain | Residue |
C | ASP253 |
C | GLN257 |
C | LYS260 |
D | LYS72 |
D | ALA74 |
D | THR75 |
D | ILE76 |
D | THR77 |
D | ARG82 |
D | ASN96 |
D | LEU288 |
D | ALA307 |
D | ALA308 |
D | HIS309 |
D | GLY310 |
D | THR311 |
D | VAL312 |
D | THR313 |
D | ARG314 |
D | HIS315 |
D | ASN328 |
D | ICT1619 |
D | HOH1748 |
D | HOH1771 |
D | HOH1825 |
D | HOH1826 |
D | HOH1922 |
site_id | AC9 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE ICT A 1616 |
Chain | Residue |
A | THR77 |
A | SER94 |
A | ARG100 |
A | ARG109 |
A | ARG132 |
A | TYR139 |
A | ASP275 |
A | NAP1515 |
A | CA1717 |
B | LYS212 |
B | THR214 |
B | ASP252 |
B | HOH1886 |
site_id | BC1 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE ICT B 1617 |
Chain | Residue |
A | LYS212 |
A | THR214 |
A | ASP252 |
B | THR77 |
B | SER94 |
B | ARG100 |
B | ARG109 |
B | ARG132 |
B | TYR139 |
B | ASP275 |
B | NAP1516 |
B | CA1718 |
site_id | BC2 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE ICT C 1618 |
Chain | Residue |
C | THR77 |
C | SER94 |
C | ARG100 |
C | ARG109 |
C | ARG132 |
C | TYR139 |
C | ASP275 |
C | NAP1517 |
C | CA1719 |
D | LYS212 |
D | THR214 |
D | ILE215 |
D | ASP252 |
site_id | BC3 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE ICT D 1619 |
Chain | Residue |
C | LYS212 |
C | THR214 |
C | ASP252 |
D | THR77 |
D | SER94 |
D | ARG100 |
D | ARG109 |
D | ARG132 |
D | TYR139 |
D | ASP275 |
D | NAP1518 |
D | CA1720 |
D | HOH1767 |
Functional Information from PROSITE/UniProt
site_id | PS00470 |
Number of Residues | 20 |
Details | IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NYDGDVqSDsvAqgy.GSLGM |
Chain | Residue | Details |
A | ASN271-MET290 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0000269|PubMed:19935646, ECO:0007744|PDB:1T09, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM, ECO:0007744|PDB:3MAP, ECO:0007744|PDB:3MAR, ECO:0007744|PDB:3MAS, ECO:0007744|PDB:4I3K, ECO:0007744|PDB:4I3L, ECO:0007744|PDB:4KZO, ECO:0007744|PDB:4L03, ECO:0007744|PDB:4L04, ECO:0007744|PDB:4L06, ECO:0007744|PDB:4UMX, ECO:0007744|PDB:4UMY, ECO:0007744|PDB:4XRX, ECO:0007744|PDB:4XS3, ECO:0007744|PDB:5DE1, ECO:0007744|PDB:5L57, ECO:0007744|PDB:5L58, ECO:0007744|PDB:5LGE, ECO:0007744|PDB:5SUN, ECO:0007744|PDB:5SVF, ECO:0007744|PDB:5TQH |
Chain | Residue | Details |
A | THR75 | |
D | THR75 | |
D | GLY310 | |
D | ASN328 | |
A | GLY310 | |
A | ASN328 | |
B | THR75 | |
B | GLY310 | |
B | ASN328 | |
C | THR75 | |
C | GLY310 | |
C | ASN328 |
site_id | SWS_FT_FI2 |
Number of Residues | 16 |
Details | BINDING: in other chain => ECO:0000269|PubMed:15173171, ECO:0007744|PDB:1T0L |
Chain | Residue | Details |
A | THR77 | |
C | SER94 | |
C | ARG109 | |
C | ARG132 | |
D | THR77 | |
D | SER94 | |
D | ARG109 | |
D | ARG132 | |
A | SER94 | |
A | ARG109 | |
A | ARG132 | |
B | THR77 | |
B | SER94 | |
B | ARG109 | |
B | ARG132 | |
C | THR77 |
site_id | SWS_FT_FI3 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0000269|PubMed:19935646, ECO:0007744|PDB:1T09, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM, ECO:0007744|PDB:3MAP, ECO:0007744|PDB:3MAR, ECO:0007744|PDB:3MAS, ECO:0007744|PDB:4I3K, ECO:0007744|PDB:4I3L, ECO:0007744|PDB:4KZO, ECO:0007744|PDB:4L03, ECO:0007744|PDB:4L04, ECO:0007744|PDB:4L06, ECO:0007744|PDB:4UMX, ECO:0007744|PDB:4UMY, ECO:0007744|PDB:4XRX, ECO:0007744|PDB:4XS3, ECO:0007744|PDB:5DE1, ECO:0007744|PDB:5L57, ECO:0007744|PDB:5LGE, ECO:0007744|PDB:5SUN, ECO:0007744|PDB:5SVF, ECO:0007744|PDB:5TQH |
Chain | Residue | Details |
A | ARG82 | |
B | ARG82 | |
C | ARG82 | |
D | ARG82 |
site_id | SWS_FT_FI4 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0007744|PDB:1T0L |
Chain | Residue | Details |
A | LYS212 | |
B | LYS212 | |
C | LYS212 | |
D | LYS212 |
site_id | SWS_FT_FI5 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000305|PubMed:15173171, ECO:0000305|PubMed:19935646, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM |
Chain | Residue | Details |
A | ASP252 | |
B | ASP252 | |
C | ASP252 | |
D | ASP252 |
site_id | SWS_FT_FI6 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0000269|PubMed:19935646, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM |
Chain | Residue | Details |
A | LYS260 | |
B | LYS260 | |
C | LYS260 | |
D | LYS260 |
site_id | SWS_FT_FI7 |
Number of Residues | 8 |
Details | BINDING: in other chain => ECO:0000305|PubMed:15173171, ECO:0000305|PubMed:19935646, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM |
Chain | Residue | Details |
A | ASP275 | |
A | ASP279 | |
B | ASP275 | |
B | ASP279 | |
C | ASP275 | |
C | ASP279 | |
D | ASP275 | |
D | ASP279 |
site_id | SWS_FT_FI8 |
Number of Residues | 8 |
Details | SITE: Critical for catalysis |
Chain | Residue | Details |
A | TYR139 | |
A | LYS212 | |
B | TYR139 | |
B | LYS212 | |
C | TYR139 | |
C | LYS212 | |
D | TYR139 | |
D | LYS212 |
site_id | SWS_FT_FI9 |
Number of Residues | 4 |
Details | MOD_RES: N-acetylserine => ECO:0007744|PubMed:22814378 |
Chain | Residue | Details |
A | SER2 | |
B | SER2 | |
C | SER2 | |
D | SER2 |
site_id | SWS_FT_FI10 |
Number of Residues | 4 |
Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:24275569 |
Chain | Residue | Details |
A | TYR42 | |
B | TYR42 | |
C | TYR42 | |
D | TYR42 |
site_id | SWS_FT_FI11 |
Number of Residues | 16 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:O88844 |
Chain | Residue | Details |
A | LYS81 | |
C | LYS224 | |
C | LYS233 | |
C | LYS243 | |
D | LYS81 | |
D | LYS224 | |
D | LYS233 | |
D | LYS243 | |
A | LYS224 | |
A | LYS233 | |
A | LYS243 | |
B | LYS81 | |
B | LYS224 | |
B | LYS233 | |
B | LYS243 | |
C | LYS81 |
site_id | SWS_FT_FI12 |
Number of Residues | 8 |
Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:O88844 |
Chain | Residue | Details |
A | LYS126 | |
A | LYS400 | |
B | LYS126 | |
B | LYS400 | |
C | LYS126 | |
C | LYS400 | |
D | LYS126 | |
D | LYS400 |
site_id | SWS_FT_FI13 |
Number of Residues | 4 |
Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
Chain | Residue | Details |
A | LYS321 | |
B | LYS321 | |
C | LYS321 | |
D | LYS321 |
site_id | SWS_FT_FI14 |
Number of Residues | 4 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:O88844 |
Chain | Residue | Details |
A | SER389 | |
B | SER389 | |
C | SER389 | |
D | SER389 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
A | VAL146 |
site_id | CSA10 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
B | THR155 |
site_id | CSA11 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
C | THR155 |
site_id | CSA12 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
D | THR155 |
site_id | CSA2 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
B | VAL146 |
site_id | CSA3 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
C | VAL146 |
site_id | CSA4 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
D | VAL146 |
site_id | CSA5 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
A | LYS212 | |
A | ASP252 |
site_id | CSA6 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
B | LYS212 | |
B | ASP252 |
site_id | CSA7 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
C | LYS212 | |
C | ASP252 |
site_id | CSA8 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
D | LYS212 | |
D | ASP252 |
site_id | CSA9 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1a05 |
Chain | Residue | Details |
A | THR155 |