5YZI
Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase complexed with Cadmium
Replaces: 2CMVFunctional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0004450 | molecular_function | isocitrate dehydrogenase (NADP+) activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005777 | cellular_component | peroxisome |
| 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 | 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 | 0042802 | molecular_function | identical protein binding |
| A | 0042803 | molecular_function | protein homodimerization activity |
| 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 | 0071071 | biological_process | regulation of phospholipid biosynthetic process |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0004450 | molecular_function | isocitrate dehydrogenase (NADP+) activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005777 | cellular_component | peroxisome |
| 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 | 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 | 0042802 | molecular_function | identical protein binding |
| B | 0042803 | molecular_function | protein homodimerization activity |
| 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 | 0071071 | biological_process | regulation of phospholipid biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 3 |
| Details | binding site for residue CD A 501 |
| Chain | Residue |
| A | ASP275 |
| A | ASP279 |
| B | ASP252 |
| site_id | AC2 |
| Number of Residues | 26 |
| Details | binding site for residue NAP A 502 |
| Chain | Residue |
| A | HIS309 |
| A | GLY310 |
| A | THR311 |
| A | VAL312 |
| A | THR313 |
| A | ARG314 |
| A | HIS315 |
| A | THR327 |
| A | ASN328 |
| A | HOH603 |
| A | HOH605 |
| A | HOH611 |
| A | HOH612 |
| A | HOH636 |
| A | HOH643 |
| A | HOH656 |
| B | ASP253 |
| B | GLN257 |
| B | LYS260 |
| B | HOH626 |
| A | LYS72 |
| A | THR75 |
| A | THR77 |
| A | ARG82 |
| A | ASN96 |
| A | ALA307 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue CD B 501 |
| Chain | Residue |
| A | ASP252 |
| B | ASP275 |
| B | ASP279 |
| B | ALA308 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue CD B 502 |
| Chain | Residue |
| B | CYS245 |
| B | GLU247 |
| B | HOH638 |
| site_id | AC5 |
| Number of Residues | 19 |
| Details | binding site for residue NAP B 503 |
| Chain | Residue |
| A | ASP253 |
| A | LYS260 |
| B | LYS72 |
| B | ALA74 |
| B | THR75 |
| B | ILE76 |
| B | THR77 |
| B | ASN96 |
| B | LEU288 |
| B | GLU306 |
| B | ALA307 |
| B | HIS309 |
| B | GLY310 |
| B | THR311 |
| B | VAL312 |
| B | THR313 |
| B | ARG314 |
| B | HIS315 |
| B | ASN328 |
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 | 10 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:29923039, ECO:0007744|PDB:5YZH, ECO:0007744|PDB:5YZI |
| Chain | Residue | Details |
| A | THR75 | |
| B | ASN328 | |
| A | ARG82 | |
| A | LYS260 | |
| A | GLY310 | |
| A | ASN328 | |
| B | THR75 | |
| B | ARG82 | |
| B | LYS260 | |
| B | GLY310 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | BINDING: in other chain => ECO:0000269|PubMed:29923039, ECO:0007744|PDB:5YZI |
| Chain | Residue | Details |
| A | THR77 | |
| A | SER94 | |
| A | ARG109 | |
| A | ARG132 | |
| B | THR77 | |
| B | SER94 | |
| B | ARG109 | |
| B | ARG132 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:29923039, ECO:0007744|PDB:5YZI |
| Chain | Residue | Details |
| A | LYS212 | |
| B | LYS212 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:29923039 |
| Chain | Residue | Details |
| A | ASP252 | |
| B | ASP252 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | BINDING: in other chain => ECO:0000305|PubMed:29923039 |
| Chain | Residue | Details |
| A | ASP275 | |
| A | ASP279 | |
| B | ASP275 | |
| B | ASP279 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | SITE: Critical for catalysis => ECO:0000250 |
| Chain | Residue | Details |
| A | TYR139 | |
| A | LYS212 | |
| B | TYR139 | |
| B | LYS212 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylserine => ECO:0000250|UniProtKB:O75874 |
| Chain | Residue | Details |
| A | SER2 | |
| B | SER2 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:O75874 |
| Chain | Residue | Details |
| A | TYR42 | |
| B | TYR42 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 8 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:23576753 |
| Chain | Residue | Details |
| A | LYS81 | |
| A | LYS224 | |
| A | LYS233 | |
| A | LYS243 | |
| B | LYS81 | |
| B | LYS224 | |
| B | LYS233 | |
| B | LYS243 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine => ECO:0007744|PubMed:23806337 |
| Chain | Residue | Details |
| A | LYS126 | |
| A | LYS400 | |
| B | LYS126 | |
| B | LYS400 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:O75874 |
| Chain | Residue | Details |
| A | LYS321 | |
| B | LYS321 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:21183079 |
| Chain | Residue | Details |
| A | SER389 | |
| B | SER389 |
