The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of two-domain protein containing predicted PHP-like metal-dependent phosphoesterase (YP_001300751.1) from Bacteroides vulgatus ATCC 8482 at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 3e38 Target Id 390183
    Molecular Characteristics
    Source Bacteroides vulgatus atcc 8482
    Alias Ids TPS7688,YP_001300751.1, BV3420, 283481 Molecular Weight 39523.85 Da.
    Residues 342 Isoelectric Point 6.02
    Sequence aqrrneiqvpdldgyttlkcdfhmhsvfsdglvwptvrvdeayrdgldaisltehieyrphkqdvvsdh nrsfdlcreqaeklgillikgseitramapghfnaiflsdsnpleqkdykdafreakkqgafmfwnhpg wdsqqpdttkwwpehtalyqegcmhgievanghlympeaiqwcldknltmigtsdihqpiqtdydfekg ehrtmtfvfakerslqgirealdnrrtaayfhelligredllrpffekcvkieevsrneqgvtlsitnv tdlvlklkktahdtllvyfrdmtlkphtrytvrigfkqgikggdvnfevtnfivapdkglkytisl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.20 Rfree 0.225
    Matthews' coefficent 2.80 Rfactor 0.172
    Waters 432 Solvent Content 56.10

    Ligand Information


    Google Scholar output for 3e38
    1. FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins
    D Roche, S Tetchner, L McGuffin - BMC bioinformatics, 2011 - biomedcentral.com
    2. Bioinformatic search for plant homologs of the protein kinase Bub1a key component of the mitotic spindle assembly checkpoint
    PA Karpov, AV Rayevsky, YB Blume - Cytology and Genetics, 2010 - Springer

    Protein Summary

    Gene BVU_3505 from Bacteroides vulgatus (strain ATCC 8482 / DSM 1447 / NCTC 11154) encodes the YP_001300751 protein that belongs to the polymerase and histidinol phosphatase group (PF02811). 

    There are two domains in each monomer of the 3e38 structure.  Based on structural similarity searches with Fold & Function Assignment System (FFAS), Dali, and SSM, the N-terminal domain (1-260) of this protein is structurally similar to PDB:1m68 (Zscr=9) and PDB:2anu (Zscr=21, topsan-2anu) with the putative active site in the PHP domain. A Tri-nuclear Zn cluster is modeled in the active site of each subunit. One phosphate anion from the crystallization condition is complexed  to the Zn-cluster, which may reveal how a phosphate group, (PO4)3-, interacts with the Zn ions. The C-terminal domain (261-363) may be structurally similar to 1DO6 and 1TEN.  There are two subunits in each asymmetric unit.

    The biomolecule of 3e38 is suggested as a tetramer according to the result from interface interaction calculation.

    Ligand Summary

    Ligand: Zn, Cacodylate ions




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