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The Open Protein Structure Annotation Network
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3ks5

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

    Title Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution. To be published
    Site JCSG
    PDB Id 3ks5 Target Id 394274
    Related PDB Ids 3ks6 
    Molecular Characteristics
    Source Agrobacterium tumefaciens str. c58
    Alias Ids TPS26618,17743486, _0090.002659_, 325471 Molecular Weight 26768.09 Da.
    Residues 249 Isoelectric Point 5.34
    Sequence mtriashrggtlefgdstphgftataamaleevefdlhptadgaivvhhdptldattdmtgaivdmtla kvktatirygagshpmtleelcalyvdshvnfrceikpgvdglpyegfvalviaglerhsmlerttfss fllasmdelwkattrprlwlvspsvlqqlgpgavietaiahsiheigvhidtadaglmaqvqaagldfg cwaahtpsqitkaldlgvkvfttdrptlaialrtehrmeasv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.05 Rfree 0.244
    Matthews' coefficent 3.49 Rfactor 0.212
    Waters 355 Solvent Content 64.72

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    This protein is now in family PF03009. 10 GDPD CL0384 along with other structures.

    Gene 17743486 (MH4068H) encodes a protein with 249 residues from AGROBACTERIUM TUMEFACIENS str. C58 with Isoelectric Point of 5.34. The NCI blast sequence alignment indicates that this protein contains a conserved domain belonging to GDPD sumperfamily.  A structural homolog search via SSM and Dali sever show that this protein is a structural homolog to glycerophosphoryl diester phosphodiesterase (1ZCC) with conserved active site, consisting of Glu34, Asp36 and Glu104.  A metal ion (Ni or Mg) is modeled in the active site. One acetate anion and water molecules complex with this metal cation.
     

    394274_1.png

    Fig. 1  Protein MH4068H is monomer with conserved active site for glycerophosphoryl

    diester phosphodiesterase

     

     

    394274_2.png

    Fig. 2  Protein MH4068H is structural homolog to  glycerophosphoryl

    diester phosphodiesterase.

     

     

    394274_3.png

     

    Fig. 3  The Active site in Protein MH4068H: a metal ion complexes with Glu34, Asp36, Glu106, UNL

    and water molecules.

     

     

     

    Reference:

    Rao, K.N.,   Bonanno, J.B.,   Burley, S.K.,   Swaminathan, S. Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit. (2006) Proteins 65: 514-518

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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