4XS3
Crystal structure of a metabolic reductase with (E)-1-benzyl-5-((1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl)pyridin-2(1H)-one
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 |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 5 |
Details | binding site for residue 42W A 501 |
Chain | Residue |
A | THR77 |
A | SER94 |
A | ARG100 |
A | ASN101 |
A | NAP502 |
site_id | AC2 |
Number of Residues | 12 |
Details | binding site for residue NAP A 502 |
Chain | Residue |
A | GLY310 |
A | THR311 |
A | THR313 |
A | ARG314 |
A | HIS315 |
A | 42W501 |
B | ALA256 |
B | LYS260 |
A | THR75 |
A | THR77 |
A | ARG82 |
A | HIS309 |
site_id | AC3 |
Number of Residues | 5 |
Details | binding site for residue 42W B 501 |
Chain | Residue |
B | THR77 |
B | LYS93 |
B | SER94 |
B | GLY97 |
B | ARG100 |
site_id | AC4 |
Number of Residues | 16 |
Details | binding site for residue NAP B 502 |
Chain | Residue |
B | LYS72 |
B | ALA74 |
B | THR75 |
B | THR77 |
B | ASN96 |
B | GLY289 |
B | GLU306 |
B | HIS309 |
B | GLY310 |
B | THR311 |
B | VAL312 |
B | THR313 |
B | ARG314 |
B | HIS315 |
B | THR327 |
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 | 6 |
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 |
site_id | SWS_FT_FI2 |
Number of Residues | 8 |
Details | BINDING: in other chain => ECO:0000269|PubMed:15173171, ECO:0007744|PDB:1T0L |
Chain | Residue | Details |
A | THR77 | |
A | SER94 | |
A | ARG109 | |
A | HIS132 | |
B | THR77 | |
B | SER94 | |
B | ARG109 | |
B | HIS132 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
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 |
site_id | SWS_FT_FI4 |
Number of Residues | 2 |
Details | BINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0007744|PDB:1T0L |
Chain | Residue | Details |
A | LYS212 | |
B | LYS212 |
site_id | SWS_FT_FI5 |
Number of Residues | 2 |
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 |
site_id | SWS_FT_FI6 |
Number of Residues | 2 |
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 |
site_id | SWS_FT_FI7 |
Number of Residues | 4 |
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 |
site_id | SWS_FT_FI8 |
Number of Residues | 4 |
Details | SITE: Critical for catalysis |
Chain | Residue | Details |
A | TYR139 | |
A | LYS212 | |
B | TYR139 | |
B | LYS212 |
site_id | SWS_FT_FI9 |
Number of Residues | 2 |
Details | MOD_RES: N-acetylserine => ECO:0007744|PubMed:22814378 |
Chain | Residue | Details |
A | SER2 | |
B | SER2 |
site_id | SWS_FT_FI10 |
Number of Residues | 2 |
Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:24275569 |
Chain | Residue | Details |
A | TYR42 | |
B | TYR42 |
site_id | SWS_FT_FI11 |
Number of Residues | 8 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:O88844 |
Chain | Residue | Details |
A | LYS81 | |
A | LYS224 | |
A | LYS233 | |
A | LYS243 | |
B | LYS81 | |
B | LYS224 | |
B | LYS233 | |
B | LYS243 |
site_id | SWS_FT_FI12 |
Number of Residues | 4 |
Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:O88844 |
Chain | Residue | Details |
A | LYS126 | |
A | LYS400 | |
B | LYS126 | |
B | LYS400 |
site_id | SWS_FT_FI13 |
Number of Residues | 2 |
Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
Chain | Residue | Details |
A | LYS321 | |
B | LYS321 |
site_id | SWS_FT_FI14 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:O88844 |
Chain | Residue | Details |
A | SER389 | |
B | SER389 |