The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of a Hypothetical Zn-dependent exopeptidase (BDI_3547) from Parabacteroides distasonis ATCC 8503 at 1.06 A resolution. To be published
    Site JCSG
    PDB Id 3tc8 Target Id 393088
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS24371,YP_001304870.1, 3.40.630.10, 323988 Molecular Weight 33924.97 Da.
    Residues 308 Isoelectric Point 5.03
    Sequence ketgnmpeikkqpiasavpdfnadsayayvanqvafgprvpntaahkacgdylaselkrfgakvyqqea iltaydgtklearniigsfdpenskrvllfahwdsrpysdhdpdpskhrtpldgaddggsgvgalleia rqigqkapgigidiiffdaedygtpefvtdytpdswclgtqfwaknphvpnytaeygilldmvggknat ffkeqqslraaapivemvwsaardlgygkyfinaaggaitddhqyvisgrnipsidiinydpesktgfa sywhtqkdnmenidretlkaagqtvleviynr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.06 Rfree 0.1315
    Matthews' coefficent 2.28 Rfactor 0.1115
    Waters 1081 Solvent Content 45.95

    Ligand Information


    Google Scholar output for 3tc8

    Protein Summary

    The protein YP_001304870.1 is annotated as leucine aminopeptidase precursor. YP_001304870.1 belongs to PFAM PF04389 Peptidase_M28


    This is a Zn-dependent peptidase. Although no Zn was found in the crystal structure (crystal id 168652), we solved another structure of this protein (crystal id 168639) which shows the presence of bound Zn.


    The monomer structure is a beta sheet surrounded by helices, shown below.

    GS10633B.png    GS10633B_168639.png


          Crystal 168652 (resolution 1.91A)                               Crystal 168639 (resolution 1.06A)


    The Zn coordination is shown below. Two Asparatate, one Histidine, one ethylene glycol, and one water molecule are coordinating the Zn ion (grey sphere).



    The DALI homologs are listed in this table.

    N PDB Z-score RMSD LALI NRES %ID Description (JCSG structures highlighted in red)
    1 3gux 41.7 0.7 243 247 64 Putative Zn-dependent Exopeptidase
    2 3pb6 31.6 2.2 262 313 22 Glutaminyl-peptide Cyclotransferase-like Protein
    3 3si2 31.4 2.3 260 322 23 Glutaminyl-peptide Cyclotransferase
    4 2ek8 31.3 2.1 251 412 22 Aminopeptidase
    5 2afu 30.4 2.3 259 322 22 Glutaminyl-peptide Cyclotransferase


    The closest structure, 3gux (cyan), is superimposed on this structure (green) to highlight the similarity, shown below.


    Ligand Summary




    No references found.

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