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The Open Protein Structure Annotation Network
PDB Keyword
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3nyy

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

    Title Crystal structure of a putative glycyl-glycine endopeptidase lytM (RUMGNA_02482) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution. To be published
    Site JCSG
    PDB Id 3nyy Target Id 416854
    Molecular Characteristics
    Source Ruminococcus gnavus atcc 29149
    Alias Ids TPS45759,ZP_02041710.1, 327492 Molecular Weight 28609.68 Da.
    Residues 251 Isoelectric Point 5.67
    Sequence vsgfqrlqkpvvsqpdfrrqpvsetmqvylkqaadpgrdvglywmatdfenrrfpgkvspsgfqklyrq wrnqtgwdayvqscraiwndvkyfpipqslddtedkisyvdswmfernyggkrghegtdimaekntpgy ypvvsmtdgvvtekgwlekggwrigitaptgayfyyahldsyaelekgdpvkagdllgymgdsgygeeg ttgefpvhlhlgiylkegteeisvnpypvlryaenarikcvysr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.60 Rfree 0.1751
    Matthews' coefficent 2.43 Rfactor 0.1491
    Waters 270 Solvent Content 49.36

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3nyy
    1. 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

    This protein (Fig 1) contains two domains, an all-helical domain 1 (29-118, red) and an endopeptidase M23-like domain 2 (green). Domain 1 shows limited similarity to goose lysozme (PDB id: 153l, Z=3.4). Domain 2 shows significant structural homology with gly-gly endopeptidase LytM (seq id 28%, rmsd 2.1). The active site is also highly similar (D156/H243/H245/H204).

     

    Domain 1 is distant from the active site, and may play a role in binding peptidoglycan.


    Fig 1. 416854 monomer

    sp0409aa.png

    Fig 2. surface, with active site residue highlighted in yellow

    sp0409aa-surf.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     sp0409aa-surf.png
    SP0409AA surface
    181.16 kB22:52, 6 Jul 2010qxuActions
     sp0409aa.png
    SP0409AA monomer
    113.42 kB22:34, 6 Jul 2010qxuActions
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