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Crystal Structure of the Human Sialidase Neu2 in Complex with 2',3'- dihydroxypropyl ether mimetic Inhibitor
Biology and Chemistry Report
2F13
  •   Structure Details   Hide

    Structure Keywords

    Keywords hydrolase
    Text SIALIDASE, NEURAMINIDASE, INFLUENZA VIRUS, DRUG DESIGN, hydrolase

    Polymeric Molecules

    Chain A
    Description Sialidase 2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 42420.0 
    Source Method genetically manipulated  
    Entity Name Neu2, Cytosolic sialidase, N-acetyl-alpha- neuraminidase 2 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    DYM  6-(2,3-DIHYDROXYPROPOXY)-5-ACETAMIDO-5,6-DIHYDRO-4-HYDROXY-4H-PYRAN-2-CARBOXYLIC ACID  C11 H17 N O8   291.26  View 
    PO4  PHOSPHATE ION  O4 P   94.97  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A NEUR2_HUMAN Q3KNW4     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    3.2.1.18        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    5975   Carbohydrate Metabolic Process  The Chemical Reactions and Pathways Involving Carbohydrates Any of a Group of Organic Compounds Based of the General Formula Cx(h2o)y. Includes the Formation of Carbohydrate Derivatives by the Addition of a Carbohydrate Residue to Another Molecule. 
    6629   Lipid Metabolic Process  The Chemical Reactions and Pathways Involving Lipids Compounds Soluble in an Organic Solvent But Not or Sparingly in an Aqueous Solvent. Includes Fatty Acids; Neutral Fats Other Fatty Acid Esters and Soaps; Long Chain (fatty) Alcohols and Waxes; Sphingoids and Other Long Chain Bases; Glycolipids Phospholipids and Sphingolipids; and Carotenes Polyprenols Sterols Terpenes and Other Isoprenoids. 
    6665   Sphingolipid Metabolic Process  The Chemical Reactions and Pathways Involving Sphingolipids Any of a Class of Lipids Containing the Long Chain Amine Diol Sphingosine or a Closely Related Base (a Sphingoid). 
    6687   Glycosphingolipid Metabolic Process  The Chemical Reactions and Pathways Involving Glycosphingolipids Any Compound with Residues of Sphingoid and At Least One Monosaccharide. 
    6689   Ganglioside Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Ganglioside a Ceramide Oligosaccharide Carrying in Addition to Other Sugar Residues One or More Sialic Residues. 
    8152   Metabolic Process  The Chemical Reactions and Pathways Including Anabolism and Catabolism by Which Living Organisms Transform Chemical Substances. Metabolic Processes Typically Transform Small Molecules But Also Include Macromolecular Processes Such As DNA Repair and Replication and Protein Synthesis and Degradation. 
    9313   Oligosaccharide Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Oligosaccharides Molecules with Between Two and (about) 20 Monosaccharide Residues Connected by Glycosidic Linkages. 
    16042   Lipid Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Lipids Compounds Soluble in an Organic Solvent But Not or Sparingly in an Aqueous Solvent. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    4308   Exo Alpha Sialidase Activity  Catalysis of the Hydrolysis of Alpha (2 >3) Alpha (2 >6) Alpha (2 >8) Glycosidic Linkages of Terminal Sialic Residues in Oligosaccharides Glycoproteins Glycolipids Colominic Acid and Synthetic Substrates. 
    16787   Hydrolase Activity  Catalysis of the Hydrolysis of Various Bonds E.g. C O C N C C Phosphoric Anhydride Bonds Etc. Hydrolase Is the Systematic Name For Any Enzyme of EC Class 3. 
    16798   Hydrolase Activity Acting On Glycosyl Bonds  Catalysis of the Hydrolysis of Any Glycosyl Bond. 
    52794   Exo Alpha (2 >3) Sialidase Activity  Catalysis of the Hydrolysis of Alpha (2 >3) Glycosidic Linkages of Terminal Sialic Residues in Substrates. 
    52795   Exo Alpha (2 >6) Sialidase Activity  Catalysis of the Hydrolysis of Alpha (2 >6) Glycosidic Linkages of Terminal Sialic Residues in Substrates. 
    52796   Exo Alpha (2 >8) Sialidase Activity  Catalysis of the Hydrolysis of Alpha (2 >8) Glycosidic Linkages of Terminal Sialic Residues in Substrates. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli bl21  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21
    Host Vector Type Plasmid
    Host Plasmid Name pGEX-2T


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    2 2q37 4759     sialidase 2 (cytosolic sialidase) NEU2    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs2233384 LS-SNP   dbSNP   A 11 S - > R Beta Ladder 37% (Exposed) 2 233897414
    rs201706789 LS-SNP   dbSNP   A 36 A - > T Beta Ladder 0% (Buried) 2 233897487
    rs144401355 LS-SNP   dbSNP   A 38 A - > V Beta Ladder 0% (Buried) 2 233897494
    rs2233385 LS-SNP   dbSNP   A 41 R - > Q Beta Ladder 32% (Intermediate) 2 233897503 DYM
    rs201184759 LS-SNP   dbSNP   A 41 R - > W Beta Ladder 32% (Intermediate) 2 233897502 DYM
    rs150159734 LS-SNP   dbSNP   A 55 R - > H Beta Ladder 17% (Intermediate) 2 233897545
    rs181881229 LS-SNP   dbSNP   A 61 A - > T Turn 38% (Exposed) 2 233897562
    rs146336403 LS-SNP   dbSNP   A 78 R - > Q Coil 38% (Exposed) 2 233898857
    rs141846686 LS-SNP   dbSNP   A 83 R - > W Beta Ladder 23% (Intermediate) 2 233898871
    rs144970536 LS-SNP   dbSNP   A 83 R - > Q Beta Ladder 23% (Intermediate) 2 233898872
    rs140090973 LS-SNP   dbSNP   A 93 A - > V Turn 48% (Exposed) 2 233898902
    rs201616110 LS-SNP   dbSNP   A 95 T - > M Turn 54% (Exposed) 2 233898908
    rs140403218 LS-SNP   dbSNP   A 123 R - > Q Beta Ladder 29% (Intermediate) 2 233898992
    rs2233390 LS-SNP   dbSNP   A 145 A - > T Helix 87% (Exposed) 2 233899057
    rs113887175 LS-SNP   dbSNP   A 152 R - > Q 3/10 Helix 70% (Exposed) 2 233899079
    rs139078223 LS-SNP   dbSNP   A 161 P - > L Bend 1% (Buried) 2 233899106
    rs2233391 LS-SNP   dbSNP   A 168 H - > N Coil 59% (Exposed) 2 233899126
    rs145457252 LS-SNP   dbSNP   A 175 V - > A Beta Ladder 0% (Buried) 2 233899148
    rs150676202 LS-SNP   dbSNP   A 175 V - > M Beta Ladder 0% (Buried) 2 233899147
    rs200746183 LS-SNP   dbSNP   A 179 Y - > H Beta Ladder 13% (Intermediate) 2 233899159 DYM
    rs144556397 LS-SNP   dbSNP   A 182 R - > W Beta Ladder 20% (Intermediate) 2 233899168
    rs2233393 LS-SNP   dbSNP   A 182 R - > Q Beta Ladder 20% (Intermediate) 2 233899169
    rs61999327 LS-SNP   dbSNP   A 184 L - > V Coil 31% (Intermediate) 2 233899174
    rs140984516 LS-SNP   dbSNP   A 203 G - > E Turn 1% (Buried) 2 233899232
    rs138984578 LS-SNP   dbSNP   A 204 R - > C Bend 66% (Exposed) 2 233899234
    rs138530805 LS-SNP   dbSNP   A 205 T - > M Bend 58% (Exposed) 2 233899238
    rs61750784 LS-SNP   dbSNP   A 207 A - > G Beta Ladder 46% (Exposed) 2 233899244
    rs141183314 LS-SNP   dbSNP   A 243 R - > T Beta Ladder 0% (Buried) 2 233899352
    rs201679476 LS-SNP   dbSNP   A 244 V - > G Beta Ladder 6% (Buried) 2 233899355
    rs146215162 LS-SNP   dbSNP   A 248 S - > R Beta Ladder 1% (Buried) 2 233899368
    rs145543414 LS-SNP   dbSNP   A 276 V - > I Beta Ladder 0% (Buried) 2 233899450
    rs201608379 LS-SNP   dbSNP   A 294 L - > V Beta Ladder 0% (Buried) 2 233899504
    rs200637515 LS-SNP   dbSNP   A 320 A - > D 3/10 Helix 6% (Buried) 2 233899583
    rs184293814 LS-SNP   dbSNP   A 328 A - > T Beta Ladder 4% (Buried) 2 233899606
    rs188986922 LS-SNP   dbSNP   A 331 S - > C Beta Ladder 36% (Exposed) 2 233899615
    rs201036365 LS-SNP   dbSNP   A 339 S - > R Beta Ladder 28% (Intermediate) 2 233899641