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The Open Protein Structure Annotation Network
PDB Keyword
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417913

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

    Site JCSG
    Status Diffraction-quality Crystals
    Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS75200,ZP_02071597.1, 323185
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS
    Ligand Information
    Ligands
    Metals
    Google Scholar output for

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    Protein Summary

    Target id 417913, a.k.a. BACUNI_03039 protein from Bacteroides uniformis ATCC 8492, is a member of a newly defined PF14869 (DUF4488) (still not in the official release) and is highly similar to another rencent JCSG structure 4gzv, so this is the second representative structure of this PFAM family. Shown below is a ribbons representation of the structure of target id 417913

     

    SP13287C_monomer.png

    The structure shows that target id 417913 is an eight-stranded beta-barrel that most likely belongs to the lipocalin SCOP fold. These types of proteins usually bind hydrophobic ligands on the interior.

    EBI-PISA indicates that a tetramer is a significant oligomerization state. Shown below is a representation of this tetrameric assembly

    SP13287C_tetramer.png

     

    A DALI structural similaritry search of the PDB databases shows that target id 417913 is similar to the following related structures:

    PDB ID Z-score rmsd (Ang) length of alignment total residues %sequence id description Ligand
    1bbp 8.9 2.4 98 173 11 MOLECULAR STRUCTURE OF THE BILIN BINDING PROTEIN (BBP) FROM PIERIS BRASSICAE AFTER REFINEMENT AT 2.0 ANGSTROMS RESOLUTION.[Ref] BILIVERDIN IX GAMMA CHROMOPHORE
    3rby 8.4 4.5 114 245 11 Crystal structure of uncharacterized protein YLR301w from Saccharomycces cerevisiae  
    3hty 8.1 2.6 82 94 9 Crystal structure of hypothetical protein BT_0869 from Bacteroides thetaiotaomicron VPI-5482 (NP_809782.1) at 1.95 A resolution (JCSG Structure)  
    2hzr 8.0 3.1 99 161 7 Crystal structure of human apolipoprotein D (ApoD)[Ref]  
    2hzq 7.8 3.1 99 166 7 Crystal structure of human apolipoprotein D (ApoD) in complex with progesterone [Ref] Progesterone
    3ebk 7.8 3.2 99 164 10 Crystal structure of major allergens, Bla g 4 from cockroaches[Ref]  
    1z24 7.7 2.8 98 189 7 The molecular structure of insecticyanin from the tobacco hornworm Manduca sexta L. at 2.6 A resolution. [Ref] BILIVERDIN IX GAMMA CHROMOPHORE
    2a8g 7.6 2.9 98 121 8 Structure of Avidin in complex with the ligand deoxyguanosine [Ref]

    2'-DEOXY-GUANOSINE

     

    N-ACETYL-D-GLUCOSAMINE
    E,
    1hbp 7.5 5.1 104 174 10 CRYSTAL STRUCTURE OF LIGANDED AND UNLIGANDED FORMS OF BOVINE PLASMA RETINOL-BINDING PROTEIN [Ref]
    RETINOL

     

    Target id 417913 shows structural similarity to another JCSG target, PDB ID 3hty.

    The structure of target id 417913 shows an unknown ligand (UNL) bound to a putative site. Shown below is a representation of this UNL superimposed on its 2fo-fc electron density contoured at 1 sigma. A molecule similar to xylose will model into this density, suggesting that this unknown ligand is a monosaccharide.

    unknown.bmp

     

    Shown below is a schematic representation of the putative active site on target id 417913. Two glutamic acid sidechains (labeled in red) are positioned similar to those found on glucoside hydroylases. This suggests that target id 417913 is a hydrolase and the unknown ligand is a sugar molecule. In addition, whereas related lipocalins bind hydrophobic ligands, target id 417913 binds more polar ligands.

     

     

     

    active_site_high_labeled.bmp

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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