The Open Protein Structure Annotation Network
PDB Keyword


    Title Crystal structure of Putative TOXIN related protein (YP_001303978.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution. To be published
    Site JCSG
    PDB Id 3k0y Target Id 394722
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25348,YP_001303978.1, 325962 Molecular Weight 25565.83 Da.
    Residues 228 Isoelectric Point 4.65
    Sequence ddnsyslgdiwiavatvvpegnnvyylrlddgdklwpaatnypnyqpkpnqralvnftiladstqsnlg gfshyikvnaihniltksiaknegaandsiygtdpvsiynnnmwigdgylniyfetlwggktahfinli qpdaendpytlefrhnayddpqytigagrvafnlsslpdtkgetvdlvvnywtsegkqayklkynsdkt kmedtsqgytndsisnitdmk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.16 Rfree 0.235
    Matthews' coefficent 2.95 Rfactor 0.203
    Waters 56 Solvent Content 58.35

    Ligand Information


    Google Scholar output for 3k0y

    Protein Summary

    The protein YP_001303978.1 is annotated as hypothetical protein BDI_2637. There is no PFAM assignment of this protein yet.


    Note from PFAM: This is now in NigD PF12667.  This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroides species. Proteins in this family are typically between 234 and 260 amino acids in length. These proteins possess an N-terminal lipoprotein attachment site. The family includes NigD a protein found in the Nig operon that encodes a bacteriocin called nigrescin. It has been suggested that NigD may be the immunity protein for nigrescin (NigC) because it is directly downstream.




    The monomer structure consits of two domains, shown below.  



    DALI Structural Homologs
    1 1qil 7.2 5.3 78 194 9 TOXIC SHOCK SYNDROME TOXIN-1
    2 2qil 7.1 5.3 79 194 9 TOXIC SHOCK SYNDROME TOXIN-1
    3 1ts4 7.1 5.3 78 194 9 TOXIC SHOCK SYNDROME TOXIN-1
    4 1aw7 7.1 5.7 79 194 9 TOXIC SHOCK SYNDROME TOXIN-1
    5 5tss 7.0 5.2 79 194 9 TOXIC SHOCK SYNDROME TOXIN-1
    6 1ts2 7.0 5.3 79 194 9 TOXIC SHOCK SYNDROME TOXIN-1
    7 4tss 6.8 5.4 79 194 9 TOXIC SHOCK SYNDROME TOXIN-1
    8 3e0e 6.8 1.9 62 91 19 REPLICATION PROTEIN A
    9 2ij0 6.8 5.3 79 194 9 TOXIC SHOCK SYNDROME TOXIN-1
    10 3dm4 6.7 2.1 62 90 10 PRIMOSOMAL REPLICATION PROTEIN N


    Although the DALI search was performed by the full length protein, the search results superpose on the N-terminal region (residues 34-108) only. Repeating the DALI search with this N-terminal domain returns the same structures.


    There is another JCSG structure YP_001299214.1 that bears a strong structural similarity to this protein. This protein is also annotated as a hypothetical protein.


    YP_001299214.1 (cyan), YP_001303978.1 (green)

    The fold type of the C- terminal domain (SH3-like barrel, SCOP) is remarkably similar to that of the structure of the kinase-associated protein B from Bacillus cereus 1Y71.

    Ligand Summary




    No references found.

    Tag page
    • No tags
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch