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3ct9

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of a Putative Zinc Peptidase (NP_812461.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.31 A resolution. To be published
    Site JCSG
    PDB Id 3ct9 Target Id 375081
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS1645,NP_812461.1, 3.40.630.10, 285251 Molecular Weight 39215.76 Da.
    Residues 355 Isoelectric Point 5.54
    Sequence mkydiptmtaeavsllkslisipsisreetqaadflqnyieaegmqtgrkgnnvwclspmfdlkkptil lnshidtvkpvngwrkdpftpreengklyglgsndagasvvsllqvflqlcrtsqnynliylasceeev sgkegiesvlpglppvsfaivgeptemqpaiaekglmvldvtatgkaghaardegdnaiykvlndiawf rdyrfekespllgpvkmsvtvinagtqhnvvpdkctfvvdirsnelysnedlfaeirkhiacdakarsf rlnssridekhpfvqkavkmgripfgsptlsdqalmsfasvkigpgrssrshtaeeyimlkeieeaigi yldlldglkl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.31 Rfree 0.253
    Matthews' coefficent 2.33 Rfactor 0.194
    Waters 192 Solvent Content 47.30

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ct9
    1. Structural basis for catalysis by the mono-and dimetalated forms of the dapE-encoded N-succinyl-L, L-diaminopimelic acid desuccinylase
    BP Nocek, DM Gillner, Y Fan, RC Holz - Journal of molecular , 2010 - Elsevier
     
    2. Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate
    AT Brunger, D Das, AM Deacon, J Grant - Section D: Biological , 2012 - scripts.iucr.org
     
    3. Mutational and structural analysis of LN-carbamoylase: new insights into a peptidase M20/M25/M40 family member.
    S Martnez-Rodrguez, A Garca-Pino - Journal of , 2012 - Am Soc Microbiol
     

    Protein Summary

    The protein is a dimer in the crystal structure and also in solution as seen by size-exclusion chormatography. There are two molecules/asu of the unit cell as show below. Each protomer has two domains, a catalytic domain that belongs to the CATH family of zinc peptidases and a second domain (that is inserted into the first domain) that forms the dimerization domain.

    PSI-BLAST indicates hits to many acetylornithine deacetylases and proteins of unknown function from many organisms. But there are no structures of proteins that are close in sequence.
    This protein shows ~21% sequence identity to PDB:1vgy over ~96% of the protein and ~27% sequence identity to PDB:2rb7 over ~72% of the protein.

    Putative active site formed by residues H73, D104, E136, E137, E161, H328 as shown below.

     

    Ligand Summary



    References

    Reviews

    References

     

    No references found.

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