The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (YP_165505.1) from Silicibacter pomeroyi DSS-3 at 1.60 A resolution. To be published
    Site JCSG
    PDB Id 3l12 Target Id 394627
    Molecular Characteristics
    Source Silicibacter pomeroyi dss-3
    Alias Ids TPS25330,YP_165505.1, _0090.002659_, 333013 Molecular Weight 34225.95 Da.
    Residues 312 Isoelectric Point 4.97
    Sequence mngfsqleglrghpsvvrvighrgargvmpentlegfaftlaagvralefdvvmtadgvpvvthnhhla namtrdgqghwltgaerqvaemtyaeiraldvggldgrtvygrrfpdqafltgihvprlgelldlcagy gdqapylllelksdpalmhdhaaraemvaavladvrryrmeprtvmhsfdwallgecrrqapdlptsyl sqlpenaddpgedsakpvgpdydrmteslpqavasaggqlwcpyfldvtpelvaeahdlglivltwtvn epedirrmattgvdgivtdypgrtqrilidmglswt
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.60 Rfree 0.187
    Matthews' coefficent 2.20 Rfactor 0.156
    Waters 701 Solvent Content 44.08

    Ligand Information


    Google Scholar output for 3l12

    Protein Summary

    Pfam note: this protein is now in family PF03009.10 GDPD CL0384 along with other structures.


    Gene SPO0236 from Silicibacter pomeroyi DSS-3 encodes the YP_165505.1 amino acid sequence, a protein with 312 residues and an isoelectric point of 4.97. The NCBI blast homology search indicates that this protein contains a conserved domain belonging to the glycerophosphoryl diester phosphodiesterase (GDPD) group (PF03009).  SCOP classifies 3l12 in the alpha/beta class, PLC-like phosphodiesterases superfamily, GDPD family. A structural similarity search via SSM and Dali servers show that 3l12 is similar to the glycerophosphoryl diester phosphodiesterase from A. tumefaciens (1ZCC) [Ref]. 3l12 predicted active site, consisting of Glu49, Asp51 and Glu148, chelates a metal ion (Mg). One glycerol and ordered water molecules contribute also to the chelation of the metal cation.




    Fig. 1  Structure 3l12 is a monomer with a predicted active site for glycerophosphoryl diester phosphodiesterase.



    Fig. 2  Structure 3l12 is structurally similar to glycerophosphoryl diester phosphodiesterase 3ks6.





    Fig. 3  Comparison with related entry 3ks6 (NOT in 3l12): Detail of the putative active site in 3ks6, where a Mg atom complexes with Glu34, Asp36, Glu104 and water molecules.

    Ligand Summary




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