3INM
Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE 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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 31 |
| Details | BINDING SITE FOR RESIDUE NDP A 501 |
| Chain | Residue |
| A | LYS72 |
| A | THR311 |
| A | VAL312 |
| A | THR313 |
| A | ARG314 |
| A | HIS315 |
| A | THR327 |
| A | ASN328 |
| A | HOH428 |
| A | HOH429 |
| A | HOH431 |
| A | ALA74 |
| A | HOH433 |
| A | HOH434 |
| A | HOH435 |
| A | HOH437 |
| A | HOH438 |
| A | AKG511 |
| A | NA522 |
| B | LEU250 |
| B | ASP253 |
| B | GLN257 |
| A | THR75 |
| B | LYS260 |
| B | HOH426 |
| A | THR77 |
| A | ARG82 |
| A | ASN96 |
| A | LEU288 |
| A | HIS309 |
| A | GLY310 |
| site_id | AC2 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE AKG A 511 |
| Chain | Residue |
| A | THR77 |
| A | SER94 |
| A | ASN96 |
| A | ARG100 |
| A | ARG109 |
| A | TYR139 |
| A | ASP275 |
| A | HOH431 |
| A | NDP501 |
| A | CA521 |
| B | LYS212 |
| B | ILE215 |
| B | ASP252 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 521 |
| Chain | Residue |
| A | ASP275 |
| A | ASP279 |
| A | HOH426 |
| A | HOH427 |
| A | AKG511 |
| B | ASP252 |
| site_id | AC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE NA A 522 |
| Chain | Residue |
| A | NDP501 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 531 |
| Chain | Residue |
| A | GLN323 |
| A | GLU324 |
| A | THR325 |
| A | ASN393 |
| A | THR394 |
| A | PHE395 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 532 |
| Chain | Residue |
| A | PHE108 |
| A | ARG109 |
| A | GLU110 |
| A | MET199 |
| A | THR292 |
| site_id | AC7 |
| Number of Residues | 27 |
| Details | BINDING SITE FOR RESIDUE NDP B 501 |
| Chain | Residue |
| A | ASP253 |
| A | GLN257 |
| A | LYS260 |
| B | LYS72 |
| B | ALA74 |
| B | THR75 |
| B | THR77 |
| B | ARG82 |
| B | ASN96 |
| B | ALA308 |
| B | HIS309 |
| B | GLY310 |
| B | THR311 |
| B | VAL312 |
| B | ARG314 |
| B | HIS315 |
| B | THR327 |
| B | ASN328 |
| B | HOH429 |
| B | HOH430 |
| B | HOH431 |
| B | HOH433 |
| B | HOH434 |
| B | HOH435 |
| B | HOH436 |
| B | AKG511 |
| B | NA522 |
| site_id | AC8 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE AKG B 511 |
| Chain | Residue |
| B | NDP501 |
| B | CA521 |
| A | ASP252 |
| B | THR77 |
| B | SER94 |
| B | ASN96 |
| B | ARG100 |
| B | ARG109 |
| B | TYR139 |
| B | ASP275 |
| B | ALA308 |
| B | HOH431 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 521 |
| Chain | Residue |
| A | ASP252 |
| B | ASP275 |
| B | ASP279 |
| B | HOH427 |
| B | HOH428 |
| B | AKG511 |
| site_id | BC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE NA B 522 |
| Chain | Residue |
| B | NDP501 |
| site_id | BC2 |
| Number of Residues | 30 |
| Details | BINDING SITE FOR RESIDUE NDP C 501 |
| Chain | Residue |
| C | ALA74 |
| C | THR75 |
| C | ILE76 |
| C | THR77 |
| C | ARG82 |
| C | ASN96 |
| C | LEU250 |
| C | ASP253 |
| C | GLN257 |
| C | LYS260 |
| C | LEU288 |
| C | ALA307 |
| C | ALA308 |
| C | HIS309 |
| C | GLY310 |
| C | THR311 |
| C | VAL312 |
| C | THR313 |
| C | ARG314 |
| C | HIS315 |
| C | ASN328 |
| C | HOH428 |
| C | HOH429 |
| C | HOH433 |
| C | HOH434 |
| C | HOH435 |
| C | HOH436 |
| C | HOH438 |
| C | AKG511 |
| C | NA522 |
| site_id | BC3 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE AKG C 511 |
| Chain | Residue |
| C | THR77 |
| C | SER94 |
| C | ASN96 |
| C | ARG100 |
| C | ARG109 |
| C | TYR139 |
| C | LYS212 |
| C | ILE215 |
| C | ASP252 |
| C | ASP275 |
| C | HOH431 |
| C | NDP501 |
| C | CA521 |
| site_id | BC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA C 521 |
| Chain | Residue |
| C | ASP252 |
| C | ASP275 |
| C | ASP279 |
| C | HOH426 |
| C | HOH427 |
| C | AKG511 |
| site_id | BC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE NA C 522 |
| Chain | Residue |
| C | ARG314 |
| C | NDP501 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL C 532 |
| Chain | Residue |
| C | PHE108 |
| C | GLU110 |
| C | ILE129 |
| C | MET199 |
| C | LYS203 |
| C | THR292 |
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 | 9 |
| 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 | |
| A | GLY310 | |
| A | ASN328 | |
| B | THR75 | |
| B | GLY310 | |
| B | ASN328 | |
| C | THR75 | |
| C | GLY310 | |
| C | ASN328 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | BINDING: in other chain => ECO:0000269|PubMed:15173171, ECO:0007744|PDB:1T0L |
| Chain | Residue | Details |
| A | THR77 | |
| C | SER94 | |
| C | ARG109 | |
| C | HIS132 | |
| A | SER94 | |
| A | ARG109 | |
| A | HIS132 | |
| B | THR77 | |
| B | SER94 | |
| B | ARG109 | |
| B | HIS132 | |
| C | THR77 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 3 |
| 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 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 3 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0007744|PDB:1T0L |
| Chain | Residue | Details |
| A | LYS212 | |
| B | LYS212 | |
| C | LYS212 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 3 |
| 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 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 3 |
| 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 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 6 |
| 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 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 6 |
| Details | SITE: Critical for catalysis |
| Chain | Residue | Details |
| A | TYR139 | |
| A | LYS212 | |
| B | TYR139 | |
| B | LYS212 | |
| C | TYR139 | |
| C | LYS212 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 3 |
| Details | MOD_RES: N-acetylserine => ECO:0007744|PubMed:22814378 |
| Chain | Residue | Details |
| A | SER2 | |
| B | SER2 | |
| C | SER2 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 3 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | TYR42 | |
| B | TYR42 | |
| C | TYR42 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:O88844 |
| Chain | Residue | Details |
| A | LYS81 | |
| C | LYS224 | |
| C | LYS233 | |
| C | 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 | 6 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:O88844 |
| Chain | Residue | Details |
| A | LYS126 | |
| A | LYS400 | |
| B | LYS126 | |
| B | LYS400 | |
| C | LYS126 | |
| C | LYS400 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 3 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS321 | |
| B | LYS321 | |
| C | LYS321 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 3 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:O88844 |
| Chain | Residue | Details |
| A | SER389 | |
| B | SER389 | |
| C | SER389 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1a05 |
| Chain | Residue | Details |
| A | THR155 |
| site_id | CSA2 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1a05 |
| Chain | Residue | Details |
| B | THR155 |
| site_id | CSA3 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1a05 |
| Chain | Residue | Details |
| C | THR155 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a05 |
| Chain | Residue | Details |
| A | LYS212 | |
| A | ASP252 |
| site_id | CSA5 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a05 |
| Chain | Residue | Details |
| B | LYS212 | |
| B | ASP252 |
| site_id | CSA6 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1a05 |
| Chain | Residue | Details |
| C | LYS212 | |
| C | ASP252 |
