6PAY
Structure of HsICDH1:Mg(II):ICT:NADPH(50%) complex reveals structural basis for observation of half-sites reactivity
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 | 18 |
| Details | binding site for residue ICT A 501 |
| Chain | Residue |
| A | THR77 |
| A | MG502 |
| A | NDP503 |
| A | HOH604 |
| A | HOH619 |
| A | HOH626 |
| A | HOH690 |
| D | LYS212 |
| D | ILE215 |
| D | ASP252 |
| A | SER94 |
| A | ASN96 |
| A | ARG100 |
| A | ARG109 |
| A | ARG132 |
| A | TYR139 |
| A | ASP275 |
| A | ALA308 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 502 |
| Chain | Residue |
| A | ASP275 |
| A | ICT501 |
| A | HOH604 |
| A | HOH666 |
| D | ASP252 |
| site_id | AC3 |
| Number of Residues | 25 |
| Details | binding site for residue NDP A 503 |
| Chain | Residue |
| A | THR75 |
| A | THR77 |
| A | ARG82 |
| A | LEU288 |
| A | HIS309 |
| A | GLY310 |
| A | THR311 |
| A | VAL312 |
| A | THR313 |
| A | ARG314 |
| A | HIS315 |
| A | ASN328 |
| A | ICT501 |
| A | FMT507 |
| A | HOH611 |
| A | HOH619 |
| A | HOH626 |
| A | HOH633 |
| A | HOH638 |
| A | HOH653 |
| A | HOH669 |
| D | ASP253 |
| D | GLN257 |
| D | LYS260 |
| D | HOH602 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | binding site for residue FMT A 504 |
| Chain | Residue |
| A | ASP225 |
| A | HOH627 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue FMT A 505 |
| Chain | Residue |
| A | LYS72 |
| A | CYS73 |
| A | ALA74 |
| A | ALA307 |
| A | SER332 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue FMT A 506 |
| Chain | Residue |
| A | ASP43 |
| B | SER41 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue FMT A 507 |
| Chain | Residue |
| A | HIS315 |
| A | SER326 |
| A | ASP375 |
| A | NDP503 |
| A | HOH603 |
| A | HOH611 |
| site_id | AC8 |
| Number of Residues | 13 |
| Details | binding site for residue ICT B 501 |
| Chain | Residue |
| B | THR77 |
| B | SER94 |
| B | ASN96 |
| B | ARG100 |
| B | ARG109 |
| B | ARG132 |
| B | TYR139 |
| B | ASP275 |
| B | MG502 |
| B | HOH644 |
| C | LYS212 |
| C | ASP252 |
| C | HOH619 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue MG B 502 |
| Chain | Residue |
| B | ASP275 |
| B | ASP279 |
| B | ICT501 |
| C | ASP252 |
| site_id | AD1 |
| Number of Residues | 2 |
| Details | binding site for residue FMT B 503 |
| Chain | Residue |
| B | ALA111 |
| B | ILE113 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue FMT B 504 |
| Chain | Residue |
| B | GLU110 |
| B | ILE129 |
| B | LYS203 |
| site_id | AD3 |
| Number of Residues | 12 |
| Details | binding site for residue ICT C 501 |
| Chain | Residue |
| B | LYS212 |
| B | ASP252 |
| C | THR77 |
| C | SER94 |
| C | ASN96 |
| C | ARG100 |
| C | ARG109 |
| C | ARG132 |
| C | TYR139 |
| C | ASP275 |
| C | MG502 |
| C | HOH637 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue MG C 502 |
| Chain | Residue |
| C | ASP279 |
| C | ICT501 |
| B | ASP252 |
| C | ASP275 |
| site_id | AD5 |
| Number of Residues | 11 |
| Details | binding site for residue ICT D 501 |
| Chain | Residue |
| A | LYS212 |
| A | ASP252 |
| D | THR77 |
| D | SER94 |
| D | ASN96 |
| D | ARG100 |
| D | ARG109 |
| D | ARG132 |
| D | TYR139 |
| D | ASP275 |
| D | MG502 |
| site_id | AD6 |
| Number of Residues | 4 |
| Details | binding site for residue MG D 502 |
| Chain | Residue |
| A | ASP252 |
| D | ASP275 |
| D | ASP279 |
| D | ICT501 |
| site_id | AD7 |
| Number of Residues | 3 |
| Details | binding site for residue FMT D 503 |
| Chain | Residue |
| D | HIS40 |
| D | TYR42 |
| D | LYS66 |
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 |
