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An Information Portal to 105097 Biological Macromolecular Structures

New strategy to analyze structures of glycopeptide antibiotic-target complexes
Biology and Chemistry Report
3RUN
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/ANTIBIOTIC
    Text antibiotic, glycopeptide, native protein ligation, fusion, carboxymethylation of cysteine, vancomycin, HYDROLASE-ANTIBIOTIC complex

    Polymeric Molecules

    Chain A
    Description LYSOZYME 
    Mutation C54T, C97A, L164A 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 19018.9 
    Source Method genetically manipulated  
    Entity Name Endolysin, Lysis protein, Muramidase 
    Chain B
    Description VANCOMYCIN 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 1150.0 
    Source Method natural source  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    BGC  BETA-D-GLUCOSE  C6 H12 O6   180.16  View 
    CL  CHLORIDE ION  Cl   35.45  View 
    IPA  ISOPROPYL ALCOHOL  C3 H8 O   60.10  View 
    MPD  (4S)-2-METHYL-2,4-PENTANEDIOL  C6 H14 O2   118.17  View 
    MRD  (4R)-2-METHYLPENTANE-2,4-DIOL  C6 H14 O2   118.17  View 
    PO4  PHOSPHATE ION  O4 P   94.97  View 
    RER  (1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose  C7 H15 N O3   161.20  View 
    TRS  2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL  C4 H12 N O3   122.14  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A ENLYS_BPT4 P00720     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    3.2.1.17      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    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. 
    9253   Peptidoglycan Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Peptidoglycans Any of a Class of Glycoconjugates Found in Bacterial Cell Walls. 
    16998   Cell Wall Macromolecule Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Macromolecules That Form Part of a Cell Wall. 
    19076   Viral Release From Host Cell  The Dissemination of Mature Viral Particles From the Host Cell E.g. by Cell Lysis or the Budding of Virus Particles From the Cell Membrane. 
    19835   Cytolysis  The Rupture of Cell Membranes and the Loss of Cytoplasm. 
    42742   Defense Response to Bacterium  Reactions Triggered in Response to the Presence of a Bacterium That Act to Protect the Cell or Organism. 
    30430   Host Cell Cytoplasm  The Cytoplasm of a Host Cell. 
    3796   Lysozyme Activity  Catalysis of the Hydrolysis of the Beta (1 >4) Linkages Between N Acetylmuramic Acid and N Acetyl D Glucosamine Residues in a Peptidoglycan and Between N Acetyl D Glucosamine Residues in Chitodextrins. 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    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. 


     
  •   Gene Details   Hide

    Natural Source

    Chain B
    Scientific Name Streptomyces orientalis  

    Genetic Source

    Chain A
    Scientific Name Enterobacteria phage t4  
    Gene e
    Host Scientific Name Escherichia coli