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Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin
Biology and Chemistry Report
4DR9
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/HYDROLASE INHIBITOR
    Text HYDROLASE-HYDROLASE INHIBITOR complex

    Polymeric Molecules

    Chain A,B,C,D
    Description Peptide deformylase 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 21333.7 
    Source Method genetically manipulated  
    Entity Name PDF, Polypeptide deformylase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    BB2  ACTINONIN  C19 H35 N3 O5   385.50  View 
    BR  BROMIDE ION  Br   79.90  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D Q5N5L5_SYNP6 Q5N5L5     

    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  3.5.1.88      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    GO ID   Ontology GO Term Definition
    6412   Translation  The Cellular Metabolic Process in Which a Protein Is Formed Using the Sequence of a Mature MRNA Molecule to Specify the Sequence of Amino Acids in a Polypeptide Chain. Translation Is Mediated by the Ribosome and Begins with the Formation of a Ternary Complex Between Aminoacylated Initiator Methionine TRNA GTP and Initiation Factor 2 Which Subsequently Associates with the Small Subunit of the Ribosome and an Mrna. Translation Ends with the Release of a Polypeptide Chain From the Ribosome. 
    5506   Iron Ion Binding  Interacting Selectively and Non Covalently with Iron (fe) Ions. 
    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. 
    42586   Peptide Deformylase Activity  Catalysis of the Reaction: Formyl L Methionyl Peptide + H2o = Formate + Methionyl Peptide. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D
    Scientific Name Synechococcus elongatus  
    Strain PCC6301
    Gene def, syc0213_d, yp_170923
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name VCID 6622


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 3199121     peptide deformylase DEF