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The Open Protein Structure Annotation Network
PDB Keyword
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3cgx

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

    Title Crystal structure of putative Nucleotide-diphospho-sugar Transferase (YP_389115.1) from Desulfovibrio desulfuricans G20 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3cgx Target Id 379240
    Molecular Characteristics
    Source Desulfovibrio desulfuricans g20
    Alias Ids TPS1734,YP_389115.1, 87988 Molecular Weight 27603.03 Da.
    Residues 241 Isoelectric Point 5.18
    Sequence msescilffvkypepgkvktrlgevvgndkaamlyrhfvqdmlqglarlhadlhicyvpgdadlpekfk awlgpqhmfaaqqgldlgermkhamqkafddgydrvvlmgsdipdypcelvqkalndlqhydaaigpaf dggyyligfrkdsfcpdvfdgirwgeadvyqptvekmrrarlevlqlpdwndvdtvwdlnvlyrtnkns sfrrsstyallrendalirqydidlpgmapveke
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.212
    Matthews' coefficent 2.41 Rfactor 0.171
    Waters 203 Solvent Content 48.98

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Sequence similarity shows that this protein, YP_389115.1, is related to COG3222: Uncharacterized protein conserved in bacteria (CD search e-value: 6e-31, ffas score: -70.800).   This protein shares sequence (ffas scores: -10.700 to -35.200) and structural similarity (SSM hits with z-scores: 6.4-18.5) to proteins in the Nucleotide-diphospho-sugar transferases Superfamily from SCOP. This similarity suggests that this protein may be an enzyme whose substrate is sugar.  Figure 1 shoes the structure of this protein.  Figure 2 shows a structural superimposition of this protein and its homolog, mannosylglycerate synthase, (PDB 2BO4). An imidazole molecule from protein expression is modeled in the structure, which should be very close to the glucose ring in the homolog.  Interface interaction calculations do not suggest that this protein is a multimer, but rather a monomer in solution.



    Figure 1. The structure of YP_389115.1.






    Figure 2. The 3D-structure alignment suggests that YP_389115.1
    is a homolog to mannosylglycerate synthase (PDB ID: 2BO4).



















     

    Ligand Summary

    Imidazole

    References

    Reviews

    References

     

    No references found.

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