4L03
Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate
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 | 33 |
| Details | BINDING SITE FOR RESIDUE NAP A 501 |
| Chain | Residue |
| A | LYS72 |
| A | HIS309 |
| A | GLY310 |
| A | THR311 |
| A | VAL312 |
| A | THR313 |
| A | ARG314 |
| A | HIS315 |
| A | ASN328 |
| A | AKG504 |
| A | HOH608 |
| A | ALA74 |
| A | HOH613 |
| A | HOH614 |
| A | HOH620 |
| A | HOH636 |
| A | HOH656 |
| A | HOH768 |
| A | HOH806 |
| A | HOH807 |
| B | LEU250 |
| B | ASP253 |
| A | THR75 |
| B | GLN257 |
| B | LYS260 |
| B | HOH609 |
| B | HOH640 |
| A | THR77 |
| A | ARG82 |
| A | ASN96 |
| A | LEU288 |
| A | ALA307 |
| A | ALA308 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 502 |
| Chain | Residue |
| A | ASP275 |
| A | ASP279 |
| A | AKG504 |
| A | HOH601 |
| A | HOH602 |
| B | ASP252 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 503 |
| Chain | Residue |
| A | ASP273 |
| A | VAL276 |
| A | GLN277 |
| B | ASP273 |
| B | GLN277 |
| site_id | AC4 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE AKG A 504 |
| Chain | Residue |
| A | THR77 |
| A | SER94 |
| A | ASN96 |
| A | ARG100 |
| A | ARG109 |
| A | ARG132 |
| A | ASP275 |
| A | ALA308 |
| A | NAP501 |
| A | CA502 |
| A | HOH602 |
| A | HOH721 |
| B | LYS212 |
| B | ASP252 |
| B | HOH609 |
| site_id | AC5 |
| Number of Residues | 33 |
| Details | BINDING SITE FOR RESIDUE NAP B 501 |
| Chain | Residue |
| A | LEU250 |
| A | ASP253 |
| A | GLN257 |
| A | LYS260 |
| A | HOH619 |
| A | HOH702 |
| A | HOH707 |
| B | LYS72 |
| B | ALA74 |
| B | THR75 |
| B | ILE76 |
| B | THR77 |
| B | ARG82 |
| B | ASN96 |
| B | ALA308 |
| B | HIS309 |
| B | GLY310 |
| B | THR311 |
| B | VAL312 |
| B | THR313 |
| B | ARG314 |
| B | HIS315 |
| B | ASN328 |
| B | AKG503 |
| B | HOH616 |
| B | HOH619 |
| B | HOH645 |
| B | HOH663 |
| B | HOH668 |
| B | HOH716 |
| B | HOH719 |
| B | HOH724 |
| B | HOH725 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 502 |
| Chain | Residue |
| A | ASP252 |
| B | ASP275 |
| B | ASP279 |
| B | AKG503 |
| B | HOH601 |
| B | HOH602 |
| site_id | AC7 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE AKG B 503 |
| Chain | Residue |
| A | ASP252 |
| B | THR77 |
| B | SER94 |
| B | ASN96 |
| B | ARG100 |
| B | ARG109 |
| B | ARG132 |
| B | ASP275 |
| B | ALA308 |
| B | NAP501 |
| B | CA502 |
| B | HOH601 |
| B | HOH616 |
| B | HOH680 |
| B | HOH681 |
| A | LYS212 |
| site_id | AC8 |
| Number of Residues | 31 |
| Details | BINDING SITE FOR RESIDUE NAP C 501 |
| Chain | Residue |
| C | LYS72 |
| C | ALA74 |
| C | THR75 |
| C | THR77 |
| C | ARG82 |
| C | ASN96 |
| C | LEU250 |
| C | ASP253 |
| C | GLN257 |
| C | LYS260 |
| C | ALA307 |
| C | ALA308 |
| C | HIS309 |
| C | GLY310 |
| C | THR311 |
| C | VAL312 |
| C | THR313 |
| C | ARG314 |
| C | HIS315 |
| C | ASN328 |
| C | AKG503 |
| C | HOH610 |
| C | HOH614 |
| C | HOH619 |
| C | HOH623 |
| C | HOH631 |
| C | HOH645 |
| C | HOH670 |
| C | HOH673 |
| C | HOH702 |
| C | HOH711 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA C 502 |
| Chain | Residue |
| C | ASP252 |
| C | ASP275 |
| C | ASP279 |
| C | AKG503 |
| C | HOH601 |
| C | HOH602 |
| site_id | BC1 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE AKG C 503 |
| Chain | Residue |
| C | THR77 |
| C | SER94 |
| C | ASN96 |
| C | ARG100 |
| C | ARG109 |
| C | ARG132 |
| C | LYS212 |
| C | ILE215 |
| C | ASP252 |
| C | ASP275 |
| C | ALA308 |
| C | NAP501 |
| C | CA502 |
| C | HOH602 |
| C | HOH610 |
| C | HOH672 |
| C | HOH675 |
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 | 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 | 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 |
