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The Open Protein Structure Annotation Network
PDB Keyword
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3d5p

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

    Title Crystal structure of putative glucan synthesis regulator of Smi1/Knr4 family (YP_211376.1) from Bacteroides fragilis NCTC 9343 at 1.45 A resolution. To be published
    Site JCSG
    PDB Id 3d5p Target Id 388451
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS1778,YP_211376.1, BIG_234, BIG_12, 60681232, 85459 Molecular Weight 16384.56 Da.
    Residues 143 Isoelectric Point 4.66
    Sequence mevieskwykkdgassasiddvekllnttlpkqyksfllwsnggegklgdnyiyiwaiedviaynhdyg iqkylqkeywafgmdgdigyilhlsdnsiyrvdlgdlditsikyiapsfddflgkaiylnfnklqnvan nnltt
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.45 Rfree 0.175
    Matthews' coefficent 2.25 Rfactor 0.156
    Waters 340 Solvent Content 45.31

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3d5p
    1. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems
    D Zhang, LM Iyer, L Aravind - Nucleic acids research, 2011 - Oxford Univ Press
     
    2. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative
    D Zhang, RF de Souza, V Anantharaman, LM Iyer - Biology , 2012 - biology-direct.com
     
    3. A New Library of Surface Patches: Design and Applications
    R Gamliel, K Kedem, R Kolodny, C Keasar - 2009 - cs.bgu.ac.il
     

    Protein Summary

    YP_211376 (BF1740) sequence is annotated as a "putative uncharacterized protein", and it belongs to Smi1/KNR4 group (PF09346). SCOP classifies 3d5p in the alpha+beta class, SMI1/KNR4-like (super)family. Structural similarity to "uncharacterized protein (PDB code: 2prv)" and "protein of unknown function (PDB code: 2icg)". 

    The biological molecule of 3d5p has been suggested as a dimer according to the calculation of interface interaction.
    Analytical size exclusion chromatography also supports the assignment of a dimer as an oligomeric state in solution.
    Figure 1. Dimer of 3d5p

    Ligand Summary

    Acetate (ACT) and glycerol (GOL) from crystallization were modeled.

    References

    Reviews

    References

     

    No references found.

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