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The Open Protein Structure Annotation Network
PDB Keyword
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3mz2

    Title Crystal structure of a Glycerophosphoryl diester phosphodiesterase (BDI_3922) from Parabacteroides distasonis ATCC 8503 at 1.55 A resolution. To be published
    Site JCSG
    PDB Id 3mz2 Target Id 396626
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS27958,YP_001305224.1, 327071 Molecular Weight 33171.70 Da.
    Residues 291 Isoelectric Point 4.81
    Sequence eeleykgmntlqisnvddlisfyqyaddriplisghrggrgkgypensmetfentlsytpatfeidprl tkdsvivlfhddtlertsngtgkvsdytweelqnfrlkdpegnitnyriptleeairwargktilildk kdvpmertaqlitdmqaepyvmitvhdgasarffyeknpnfmfeafvktkeavqdyedngipwshimay vgpkitpevrevidmlhergvmcmistapsddklstpesraeayrmiirqgvdiiesdrpievaeaiss lipvssskgkffstl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.55 Rfree 0.197
    Matthews' coefficent 2.01 Rfactor 0.166
    Waters 541 Solvent Content 38.77

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3mz2

    Protein Summary

    The protein YP_001305224.1 is annotated as Glycerophosphoryl diester phosphodiesterase. YP_001305224.1 belongs to PFAM PF03009 GDPD. 

    The monomer structure is a barrel flanked by helices, shown below.

    PX4068D.png

     

    Theer are several structural homologs of this protein, shown below in the table.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE (JCSG structures highlighted in red)
    1 3i10 26.0 2.5 256 278 24 PUTATIVE GLYCEROPHOSPHORYL DIESTER
    2 2pz0 23.2 2.5 227 243 26 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    3 1zcc 22.8 2.9 230 240 20 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    4 2o55 21.8 2.7 228 254 24 PUTATIVE GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    5 3l12 21.7 2.8 240 295 20 PUTATIVE GLYCEROPHOSPHORYL DIESTER
    6 2oog 21.3 2.9 232 267 22 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    7 2p76 21.1 2.9 231 267 22 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    8 3ks6 21.0 3.0 225 246 17 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    9 3ks5 20.9 2.9 225 247 17 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    10 3ch0 20.6 2.9 223 272 20 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE

     

    The superposition of this protein (green) with 3i10 (orange) is shown below.

    PX4068D_3i10.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     PX4068D.png
    No description
    110.21 kB19:05, 4 Mar 2010abhinavkActions
     PX4068D_3i10.png
    No description
    161.29 kB19:05, 4 Mar 2010abhinavkActions
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