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1npd

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

    Title The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase. J.Biol.Chem. 278 19176-19182 2003
    Site NESGC
    PDB Id 1npd Target Id ER24
    Molecular Characteristics
    Source Escherichia coli
    Alias Ids TPS8837,3.40.192.10, PF08501, PF01488, 3.40.50.720 Molecular Weight 31226.14 Da.
    Residues 288 Isoelectric Point 5.03
    Sequence mdvtakyeliglmaypirhslspemqnkalekaglpftymafevdndsfpgaieglkalkmrgtgvsmp nkqlaceyvdeltpaaklvgaintivnddgylrgyntdgtghiraikesgfdikgktmvllgaggasta igaqgaieglkeiklfnrrdeffdkalafaqrvnentdcvvtvtdladqqafaealasadiltngtkvg mkpleneslvndisllhpgllvtecvynphmtkllqqaqqagcktidgygmllwqgaeqftlwtgkdfp leyvkqvmgfga
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.30 Rfree 0.274
    Matthews' coefficent 2.12 Rfactor 0.217
    Waters 319 Solvent Content 41.51

    Ligand Information
    Ligands NAD (NICOTINAMIDE-ADENINE-DINUCLEOTIDE) x 2
    Metals

    Jmol

     
    Google Scholar output for 1npd
    1. Progress of structural genomics initiatives: an analysis of solved target structures
    AE Todd, RL Marsden, JM Thornton - Journal of molecular , 2005 - Elsevier
     
    2. Statistical analysis and prediction of proteinprotein interfaces
    AJ Bordner, R Abagyan - Proteins: Structure, Function, and , 2005 - Wiley Online Library
     
    3. Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets
    C Abergel, B Coutard, D Byrne, S Chenivesse - Journal of structural and , 2003 - Springer
     
    4. Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli
    HA Lindner, G Nadeau, A Matte, G Michel - Journal of Biological , 2005 - ASBMB
     
    5. Continuous optimization methods for structure alignments
    R Andreani, JM Martnez, L Martnez, F Yano - Mathematical Programming, 2008 - Springer
     
    6. Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism
    B Bagautdinov, N Kunishima - Journal of molecular biology, 2007 - Elsevier
     
    7. Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism
    J Gan, Y Wu, P Prabakaran, Y Gu, Y Li - Biochemistry, 2007 - ACS Publications
     
    8. A fold-recognition approach to loop modeling
    C Levefelt, D Lundh - Journal of molecular modeling, 2006 - Springer
     
    9. A new approach to assess and predict the functional roles of proteins across all known structures
    ES Julfayev, RJ McLaughlin, YP Tao - Journal of structural and , 2011 - Springer
     
    10. Studies on the inference of protein binding regions across fold space based on structural similarities
    J Teyra, J Hawkins, H Zhu - : Structure, Function, and , 2011 - Wiley Online Library
     
    11. Protein Structure Database for Structural Genomics Group
    JY Lau - 2005 - www-nmr.cabm.rutgers.edu
     

    Protein Summary


    Ligand Summary

    Reviews

    References

     

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