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3no6

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

    Title Crystal structure of a putative thiaminase II (SE1693) from Staphylococcus epidermidis ATCC 12228 at 1.65 A resolution. To be Published
    Site JCSG
    PDB Id 3no6 Target Id 394358
    Molecular Characteristics
    Source Staphylococcus epidermidis atcc 12228
    Alias Ids TPS29516,NP_765248.1, _0077.002005_, 332996 Molecular Weight 26898.17 Da.
    Residues 229 Isoelectric Point 4.88
    Sequence mtfskelreasrpiiddiyndgfiqdllagklsnqavrqylradasylkeftniyamlipkmssmedvk flveqiefmlegeveahevladfinepyeeivkekvwppsgdhyikhmyfnafarenaaftiaamapcp yvyavigkramedpklnkesvtskwfqfystemdelvdvfdqlmdrltkhcsetekkeikenflqstih erhffnmayinekweyggnnne
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.65 Rfree 0.190
    Matthews' coefficent 2.25 Rfactor 0.166
    Waters 790 Solvent Content 45.35

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3no6
    1. Assessment of ligand_binding residue predictions in CASP9
    T Schmidt, J Haas, TG Cassarino - Structure, Function, and , 2011 - Wiley Online Library
     
    2. Purification, crystallization and preliminary X-ray diffraction analysis of the thiaminase type II from Staphylococcus aureus
    A Begum, J Drebes, M Perbandt - Section F: Structural , 2010 - scripts.iucr.org
     
    3. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     

    Protein Summary

    The protein NP_765248.1 is annotated as  putative thiaminase II.  NP_765248.1 belongs to PFAM PF03070 TENA_THI-4.

    The monomer structure, displayed below.

    MH10870A.png

     

    The most likely biomolecule in solution is a tetramer as suggested by Size Exclusion experiment and crystal packing.

    MH10870A_tetramer.png

     

    Some ot the top DALi hits of this protein is tabulated below.

    N PDB Z-score RMSD LALI NRES %ID Description
    1 3ibx 27.4 2.2 219 221 21 PUTATIVE THIAMINASE II
    2 2rd3 27.0 2.0 216 218 21 TRANSCRIPTIONAL REGULATOR
    3 1to9 26.6 2.3 220 223 24 THI-4 PROTEIN
    4 2qcx 26.4 2.2 217 222 23 TRANSCRIPTIONAL ACTIVATOR TENA
    5 1tyh 26.4 2.3 217 221 24 TRANSCRIPTIONAL ACTIVATOR TENA
    6 1yaf 26.3 2.2 215 219 23 TRANSCRIPTIONAL ACTIVATOR TENA
    7 1yak 26.2 2.3 217 219 23 TRANSCRIPTIONAL ACTIVATOR TENA
    8 1udd 24.5 2.2 209 213 21 TRANSCRIPTIONAL REGULATOR
    9 2gm7 23.8 2.3 208 212 22 TENA HOMOLOG/THI-4 THIAMINASE
    10 2gm8 23.7 2.4 209 215 22 TENA HOMOLOG/THI-4 THIAMINASE

     

    An imidazole molecule has been modeled in the thiamine binding site of the molecule as shown below. Resdiues D44, Y141, and Y167 are implicated in the thiamine binding (http://www.genome.jp/dbget-bin/www_b...rot+TENA_STAES).

    act_site.png

    A Thiamine like ligand, HMH (4-amino-2-methylpyrimidin-5-yl)methanol, binds to another Thiaminase structure 2gm8, and an imidazole is bound in identical position to another JCSG structure 2qzc. The binding site is very well conserved among these two proteins and this target.

    Ligand Summary

    Reviews

    References

     

    No references found.

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