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3dmc

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

    Title Crystal structure of a NTF2-like Protein (YP_322774.1) from ANABAENA VARIABILIS ATCC 29413 at 1.65 A resolution. To be published
    Site JCSG
    PDB Id 3dmc Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS9371,YP_322774.1, 3.10.450.50, 104459
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.13 Rfactor 0.175
    Waters
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    Solvent Content 42.38

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3dmc
    1. DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in
    D Lagorce, T Pencheva, BO Villoutreix - BMC Chemical , 2009 - w09.biomedcentral.com
     
    2. Conformational sampling and energetics of drug-like molecules
    N Foloppe, IJ Chen - Current medicinal chemistry, 2009 - ingentaconnect.com
     
    3. MED-3DMC
    O Sperandio, M Souaille, F Delfaud, MA Miteva - European journal of , 2009 - Elsevier
     
    4. Confab-Systematic generation of diverse low-energy conformers
    NM O'Boyle, T Vandermeersch, CJ Flynn - Journal of , 2011 - Springer
     
    5. Bioactive conformational generation of small molecules: A comparative analysis between force-field and multiple empirical criteria based methods
    F Bai, X Liu, J Li, H Zhang, H Jiang, X Wang - BMC , 2010 - biomedcentral.com
     
    6. Protein Physics by Advanced Computational Techniques: Conformational Sampling and Folded State Discrimination
    PC Tejada - 2011 - sissa.it
     
    7. Identifying and characterizing binding sites and as-sessing druggability.
    TA Halgren - Bioorg. Med. Chem, 2009 - Wiley Online Library
     
    8. AMMOS Software: Method and Application.
    T Pencheva, D Lagorce, I Pajeva, BO Villoutreix - Methods in molecular , 2012 - Springer
     
    9. Frog2: Efficient 3D conformation ensemble generator for small compounds
    MA Miteva, F Guyon, P Tuffry - Nucleic acids research, 2010 - Oxford Univ Press
     
    10. Three-dimensional structure generators of drug-like compounds: DG-AMMOS, an open-source package
    D Lagorce, BO Villoutreix - Expert Opinion on Drug , 2011 - ingentaconnect.com
     
    11. A New Library of Surface Patches: Design and Applications
    R Gamliel, K Kedem, R Kolodny, C Keasar - 2009 - cs.bgu.ac.il
     

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    Protein Summary

    The Ava_2261 gene from Anabaena variabilis atcc 29413 encodes the YP_322774 protein that shows a weak hit with the  "limonene-1,2-epoxide hydrolase catalytic domain" group (PF07858, EC 3.3.2.8).

    3dmc belongs to the SCOP NTF2-like superfamily and adopts a cystatin-like fold. It shows structural similarity to 3i0y, a putative polyketide cyclase. For more information on the structure [Ref] and function [Ref] of this enzyme, see the associated references.

    Ligand Summary

    Reviews

    References

     

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