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Crystal structure of human beta secretase complexed with NVP-AMK640
Biology and Chemistry Report
1YM4
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/HYDROLASE INHIBITOR
    Text BETA-SECRETASE, MEMAPSIN2, ALZHEIMER'S DISEASE, ASPARTIC PROTEASE, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex

    Polymeric Molecules

    Chain A,B,C
    Description Beta-secretase 1 
    Fragment UNP residues 48-453 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 45435.4 
    Source Method genetically manipulated  
    Entity Name Beta-site APP cleaving enzyme 1, Beta-site amyloid precursor protein cleaving enzyme 1, Aspartyl protease 2, Asp 2, ASP2, Membrane-associated aspartic protease 2, Memapsin-2 
    Chain X,Y,Z
    Description NVP-AMK640 INHIBITOR 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 642.7 
    Source Method synthetic  

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C BACE1_HUMAN A0M8W7     

    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)
    A B C  3.4.23.46        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C
    GO ID   Ontology GO Term Definition
    6508   Proteolysis  The Hydrolysis of Proteins Into Smaller Polypeptides And/or Amino Acids by Cleavage of Their Peptide Bonds. 
    4190   Aspartic Type Endopeptidase Activity  Catalysis of the Hydrolysis of Internal Alpha Peptide Bonds in a Polypeptide Chain by a Mechanism in Which a Water Molecule Bound by the Side Chains of Aspartic Residues At the Active Center Acts As a Nucleophile. 


    Protein Analyses

    Measured Binding Affinities   

     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Type Plasmid
    Host Plasmid Name pET24


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    11 11q23.2-q23.3 23621     beta-site APP-cleaving enzyme 1 BACE1    

    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
    rs17857093 LS-SNP   dbSNP   A 57 S - > F Coil 8% (Buried) 11 117166061
    rs138138981 LS-SNP   dbSNP   A 61 R - > Q Beta Ladder 68% (Exposed) 11 117166049
    rs200733909 LS-SNP   dbSNP   A 64 R - > W Beta Ladder 87% (Exposed) 11 117166041
    rs151257620 LS-SNP   dbSNP   A 88 P - > T Turn 42% (Exposed) 11 117165969
    rs200695125 LS-SNP   dbSNP   A 171 G - > R Beta Ladder 26% (Intermediate) 11 117164598
    rs201550686 LS-SNP   dbSNP   A 182 S - > W Turn 5% (Buried) 11 117163882
    rs145565779 LS-SNP   dbSNP   A 202 I - > V Coil 5% (Buried) 11 117163823
    rs28989503 LS-SNP   dbSNP   A 204 V - > A Beta Ladder 8% (Buried) 11 117163816
    rs140050693 LS-SNP   dbSNP   A 211 Q - > H Beta Ladder 67% (Exposed) 11 117163794
    rs149860623 LS-SNP   dbSNP   A 274 T - > S Coil 47% (Exposed) 11 117161704
    rs139977300 LS-SNP   dbSNP   A 328 S - > P Bend 35% (Intermediate) 11 117161303