The Open Protein Structure Annotation Network
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    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


    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


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


    Ligand Summary




    No references found.

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    Files (2)

    FileSizeDateAttached by 
    SP0409AA surface
    181.16 kB22:52, 6 Jul 2010qxuActions
    SP0409AA monomer
    113.42 kB22:34, 6 Jul 2010qxuActions
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