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The Open Protein Structure Annotation Network
PDB Keyword
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3nmb

    Title Crystal structure of a putative sugar hydrolase (BACOVA_03189) from Bacteroides ovatus at 2.40 A resolution. To be published
    Site JCSG
    PDB Id 3nmb Target Id 416742
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS33735,ZP_02066194.1, 327441 Molecular Weight 29121.88 Da.
    Residues 259 Isoelectric Point 4.83
    Sequence qeepskvalsyskslkapetdslnlpvdengyitifdgetfngwrgygkdrvptkwtiedgcikfngsg ggeaqdgdggdlifahkfknfelelewkvakgsnsgilylaqevtskdkdgndvlepiyisapeyqild nanhpdaklgkdnnrqsaslydmipavpqnskpfgewnkakimvykgtvvhgqndenvleyhlwtkqwt dmlqaskfsedkwplafellnncggenhegfiglqdhgddvwfrnirvkvld
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.40 Rfree 0.2166
    Matthews' coefficent 4.02 Rfactor 0.1694
    Waters 192 Solvent Content 69.43

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3nmb
    1. Assessment of ligand_binding residue predictions in CASP9
    T Schmidt, J Haas, TG Cassarino - Structure, Function, and , 2011 - Wiley Online Library
     
    2. Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement
    A Roy, Y Zhang - Structure, 2012 - Elsevier
     
    3. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     

    Protein Summary

    The protein ZP_02066194.1 is annotated as hypothetical protein BACOVA_03189. ZP_02066194.1 belongs to PFAM PF06439 DUF1080. This a family of proteins of unknown function. The DUF is part of clan CL0004, concanavalin like and it is expected to be a form of a carbohydrate binding domain.

     

    The monomer structure is shown below which consists of a beta-sandwich.

    SP13645A.png

     

    The structural homologs (see table below) suggest that this protein could be a putative sugar hydrolase.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID Description (JCSG structures highlighted in red)
    1 3h3l 30.6 1.5 209 223 52 Putative Sugar Hydrolase
    2 3hbk 28.9 1.7 214 231 38 Putative Glycosyl Hydrolase
    3 3imm 21.6 2.2 187 197 25 Putative Secreted Glycosylhydrolase
    4 1oq1 14.5 3.1 181 223 10 Protein Yesu
    5 3d6e 13.7 2.8 164 186 10 Beta-glucanase
    6 2a6x 12.6 2.8 163 219 7 Emp46p
    7 3fby 12.5 3.4 164 535 12 Cartilage Oligomeric Matrix Protein
    8 2a6w 12.5 2.8 165 219 7 Emp46p
    9 2a6v 12.5 2.8 164 217 7 Emp46p
    10 1gv9 12.5 2.8 162 223 16 P58/ergic-53

     

     

    A superposition of this protein (green) with 3h3l (magenta) is shown below.

    SP13645A_3h3l.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     SP13645A.png
    No description
    69.74 kB23:38, 26 Apr 2010abhinavkActions
     SP13645A_3h3l.png
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    92.1 kB23:38, 26 Apr 2010abhinavkActions
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