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 transcriptional regulator containing a LuxR DNA binding domain (NP_811094.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.04 A resolution. To be published
    Site JCSG
    PDB Id 3clo Target Id 383272
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS1770,NP_811094.1, 88499 Molecular Weight 29573.30 Da.
    Residues 257 Isoelectric Point 5.87
    Sequence mdvlqkeidevyathptahealdngiveqhqqfvrsltevnggcavisdlsnrksyvtvhpwanflglt peeaalsvidsmdedciyrrihpedlvekrlmeykffqktfsmspgerlkyrgrcrlrmmnekgvyqyi dnlvqimqntpagnvwlifclyslsadqrpeqgiyatitqmergevetlslseehrnilserekeilrc irkglsskeiaatlyisvntvnrhrqnileklsvgnsieacraaelmkll
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 2.04 Rfree 0.217
    Matthews' coefficent 3.64 Rfactor 0.187
    Waters 494 Solvent Content 66.25

    Ligand Information


    Google Scholar output for 3clo
    1. Increased detection in Australia and Singapore of a novel influenza A (H1N1) 2009 variant with reduced oseltamivir and zanamivir sensitivity due to a S247N
    AC Hurt, RT Lee, SK Leang, L Cui, Y Deng - Euro , 2011 - eurosurveillance.eu
    2. Homology modeling, docking, and molecular dynamics reveal HR1039 as a potent inhibitor of 2009 A (H1N1) influenza neuraminidase
    YT Wang, C Chan, ZY Su, CL Chen - Biophysical chemistry, 2010 - Elsevier
    CH Andrade, GHG Trossini, EI Ferreira - Revista Eletrnica de , 2010 - revistas.ufg.br
    4. Mutations I117V and I117M and Oseltamivir Sensitivity of Pandemic (H1N1) 2009 Viruses
    AC Hurt, SK Leang, DJ Speers, IG Barr - Emerging infectious , 2012 - flu.org.cn
    5. Combining molecular simulation techniques to predict the binding modes of oseltamivir, zanamivir and natural herb products with the neuramindase of the H1N1
    YT Wang, C Chan - Bioinformatics and Biomedical Technology , 2010 - ieeexplore.ieee.org

    Protein Summary

    NP_811094.1 contains two domains (1-197, 198-257). The C-terminal domain contains a LuxR DNA binding domain and  has well defined structural homologs (rmsd<1 and seq id ~30), the N-terminal domain seems to be novel. There are no known structures which are highly homologous to the N-terminal domain.

    This protein is likely to function as a dimer. The two DNA binding domains of NP_811094.1 are placed in an interesting fashion. By superimposing the LuxR domains of this proteins and NarL-C/DNA complex, two strands of dsDNA can be approximately positioned onto NP_811094.1. Thus it appears that this protein severly bends the dsDNA or that it has to bind to separate strands of dsDNA.

    Fig 1. NP_811094.1 with modeled dsDNA

    This protein is likely to function as transcription regulator. The N-terminal domain can bind small molecule substrate. There are very few known sequence homologs for the N-terminal domain. It is thus not easy to infer whether it is the substrate binding site.

    Fig 2. Sequence conservation on NP_811094.1 dimer surface. cyan-least conserved, magenta-most conserved residues.

    Ligand Summary





    No references found.

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