The Open Protein Structure Annotation Network
PDB Keyword


    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


    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.





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