The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of periplasmic glycerophosphodiester phosphodiesterase from Escherichia coli. To be Published
    Site NYSGXRC
    PDB Id 1ydy Target Id NYSGXRC-T1974
    Molecular Characteristics
    Source Escherichia coli
    Alias Ids TPS8258,16130174 Molecular Weight 40841.33 Da.
    Residues 358 Isoelectric Point 5.38
    Sequence mkltlknlsmaimmstivmgssamaadsnekiviahrgasgylpehtlpakamayaqgadyleqdlvmt kddnlvvlhdhyldrvtdvadrfpdrarkdgryyaidftldeikslkftegfdiengkkvqtypgrfpm gksdfrvhtfeeeiefvqglnhstgknigiypeikapwfhhqegkdiaaktlevlkkygytgkddkvyl qcfdadelkriknelepkmgmelnlvqliaytdwnetqqkqpdgswvnynydwmfkpgamkqvaeyadg igpdyhmlieetsqpgnikltgmvqdaqqnklvvhpytvrsdklpeytpdvnqlydalynkagvnglft dfpdkavkflnke
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.228
    Matthews' coefficent 2.30 Rfactor 0.187
    Waters 785 Solvent Content 45.80

    Ligand Information
    Ligands GOL (GLYCEROL) x 2
    Metals CA (CALCIUM) x 2


    Google Scholar output for 1ydy
    1. Prediction of transition metal_binding sites from apo protein structures
    M Babor, S Gerzon, B Raveh - Proteins: Structure, , 2008 - Wiley Online Library
    2. An iterative knowledge_based scoring function for proteinprotein recognition
    SY Huang, X Zou - Proteins: Structure, Function, and , 2008 - Wiley Online Library
    3. The Structure and Function of a Novel Glycerophosphodiesterase from Enterobacter aerogenes
    CJ Jackson, PD Carr, JW Liu, SJ Watt, JL Beck - Journal of molecular , 2007 - Elsevier
    4. Structural insights into the catalytic mechanism of sphingomyelinases D and evolutionary relationship to glycerophosphodiester phosphodiesterases
    MT Murakami, M Freitas Fernandes-Pedrosa - Biochemical and , 2006 - Elsevier
    5. The glycerophosphoryl diester phosphodiesterase-like proteins SHV3 and its homologs play important roles in cell wall organization
    S Hayashi, T Ishii, T Matsunaga - Plant and cell , 2008 - Jpn Soc Plant Physiol
    6. Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria
    MHJ Cordes, GJ Binford - Bioinformatics, 2006 - Oxford Univ Press
    7. Genomic organization, characterization, and molecular 3D model of GDE1, a novel mammalian glycerophosphoinositol phosphodiesterase
    AS Bachmann, FF Duennebier, G Mocz - Gene, 2006 - Elsevier
    8. Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit
    KN Rao, JB Bonanno, SK Burley - Proteins: Structure, , 2006 - Wiley Online Library
    9. Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion_dependent enzyme: Insight into the
    L Shi, JF Liu, XM An, DC Liang - Proteins: Structure, Function, , 2008 - Wiley Online Library
    10. Escherichia coli cytosolic glycerophosphodiester phosphodiesterase (UgpQ) requires Mg2+, Co2+, or Mn2+ for its enzyme activity
    N Ohshima, S Yamashita, N Takahashi - Journal of , 2008 - Am Soc Microbiol
    11. Closed loop folding units from structural alignments: Experimental foldons revisited
    SV Chintapalli, BK Yew, CJR Illingworth - Journal of , 2010 - Wiley Online Library

    Protein Summary

    Ligand Summary




    No references found.

    Tag page
    • No tags

    Files (0)

    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch