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The Open Protein Structure Annotation Network
PDB Keyword
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4n0r

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

    Title Crystal structure of a putative glycoside hydrolase (BVU_0362) from Bacteroides vulgatus ATCC 8482 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 4n0r Target Id 418078
    Molecular Characteristics
    Source Bacteroides vulgatus atcc 8482
    Alias Ids TPS76599,YP_001297703.1, 531859 Molecular Weight 59392.72 Da.
    Residues 512 Isoelectric Point 6.94
    Sequence qdkvecwdrfelsfkqvtkgnpfdirlsatfvcgkekktvegfydgentyrirfmpavagewryvtsss igamngrkgtftvipagkdnhgmvlvdgehnfkyadgtryypmgttayawthmkettqeatlksfgeag fnkvrmcvfpknyslvkdepalypfeiektikdkegnerkewdfdrfdpaffqhlekridqlnrlgiea dlilfhpydkgrwgfdamsnevnvryikyitarlasfrnvwwsmanewdyvkaktvddwklltktvven dpyrhlcsihgatatyfdywmpefthvsiqdeapvlsstasatlrkiyrkpvicdevgyegnlpyrwgr lspqqmtcfilngllggiyvthgecyqqgnepifwaqggslkgeswkrvkflrtiieaaphplemadis rdlvtstagpdyylvnmgkdvkgfwtfnlpvknadynklqknkrfkveiidvwamtvteypvifettee ldyrvfdihhrgvripdapyivlritevk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.80 Rfree 0.1796
    Matthews' coefficent 2.87 Rfactor 0.1501
    Waters 1293 Solvent Content 57.13

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    This protein, BVU_0362 (Uniprot A6KXB7_BACV8) is likely a carbohydrate-binding protein. It has been classified in Pfam DUF4038 (PF13204). JCSG has solved another structure from this Pfam with only 11% seq id but FFAS score of -70, PDB id 3kzs(topsan entry).

    dbCAN annotates BVU_0362 as a GH5 family protein (Glycosidic Hydrolase family 5). Here is some CAZypedia information on GH5.

    There are 2 molecules in the asymmetric unit. An endogenous NAG-like carbohydrate molecule is present in the putative binding site. The density looks NAG-like, but due to the presence of an anomalous difference Fourier peak, it was modeled as a Ni ion and UNL (unknown ligand). It could also be a larger UNL with an anomalously scattering element or a partially occupied larger ligand with an overlapping partially occupied hydrated Ni ion.

    While there is only 11% identity to 3kzs, a number of the residues lining the pocket with the bound UNL are conserved --e.g. H308, E276, E354, Q328, Y357.
    (3kzs has an MPD bound in the pocket).
     

    Fig2.png

    Fig1.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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