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Crystal structure of a complex between Actinomadura R39 DD-peptidase and a trifluoroketone inhibitor
Biology and Chemistry Report
3ZCZ
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text HYDROLASE, INHIBITOR, PEPTIDOGLYCAN

    Polymeric Molecules

    Chain A,B,C,D
    Description D-ALANYL-D-ALANINE CARBOXYPEPTIDASE 
    Fragment RESIDUES 50-516 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 47704.6 
    Source Method natural source  
    Entity Name DD-CARBOXYPEPTIDASE, DD-PEPTIDASE, PENICILLIN-BINDING PROTEIN, PBP 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MG  MAGNESIUM ION  Mg   24.31  View 
    SO4  SULFATE ION  O4 S   96.06  View 
    TFR  (2R)-2-amino-7-oxo-7-{[(2R,3S)-4,4,4-trifluoro-3-hydroxybutan-2-yl]amino}heptanoic acid  C11 H19 F3 N2 O4   300.28  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D DAC_ACTSP P39045     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B C D  3.4.16.4      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    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. 
    8360   Regulation of Cell Shape  Any Process That Modulates the Surface Configuration of a Cell. 
    9252   Peptidoglycan Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Peptidoglycans Any of a Class of Glycoconjugates Found in Bacterial Cell Walls. 
    46677   Response to Antibiotic  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Antibiotic Stimulus. an Antibiotic Is a Chemical Substance Produced by a Microorganism Which Has the Capacity to Inhibit the Growth of or to Kill Other Microorganisms. 
    71555   Cell Wall Organization  A Process That Results in the Assembly Arrangement of Constituent Parts or Disassembly of the Cell Wall the Rigid or Semi Rigid Envelope Lying Outside the Cell Membrane of Plant Fungal and Most Prokaryotic Cells Maintaining Their Shape and Protecting Them From Osmotic Lysis. 
    5576   Extracellular Region  The Space External to the Outermost Structure of a Cell. For Cells Without External Protective or External Encapsulating Structures This Refers to Space Outside of the Plasma Membrane. This Term Covers the Host Cell Environment Outside an Intracellular Parasite. 
    4180   Carboxypeptidase Activity  Catalysis of the Hydrolysis of the Terminal or Penultimate Peptide Bond At the C Terminal End of a Peptide or Polypeptide. 
    4185   Serine Type Carboxypeptidase Activity  Catalysis of the Hydrolysis of a Peptide Bond Not More Than Three Residues From the C Terminus of a Polypeptide Chain by a Catalytic Mechanism That Involves a Catalytic Triad Consisting of a Serine Nucleophile That Is Activated by a Proton Relay Involving an Acidic Residue (e.g. Aspartate or Glutamate) and a Basic Residue (usually Histidine). 
    8233   Peptidase Activity  Catalysis of the Hydrolysis of a Peptide Bond. a Peptide Bond Is a Covalent Bond Formed When the Carbon Atom From the Carboxyl Group of One Amino Acid Shares Electrons with the Nitrogen Atom From the Amino Group of a Second Amino Acid. 
    9002   Serine Type D Ala D Ala Carboxypeptidase Activity  Catalysis of the Reaction: (ac)2 L Lys D Alanyl D Alanine + H2o = (ac)2 L Lys D Alanine + D Alanine. 
    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. 


     
  •   Gene Details   Hide

    Natural Source

    Chain A,B,C,D
    Scientific Name Actinomadura sp. r39