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 putative glucoamylase (YP_210071.1) from Bacteroides fragilis NCTC 9343 at 2.12 A resolution. To be published
    Site JCSG
    PDB Id 3eu8 Target Id 390129
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS7672,YP_210071.1, 88046 Molecular Weight 48501.26 Da.
    Residues 429 Isoelectric Point 5.82
    Sequence vackpkekpssatsltddalmdtvqrrtfnyfwdaaepnsglareryhmdgeypaggpeivtsggsgfg imailagidrgyvsreeglrrmekivgflekadrfkgayphwwngetghvqpfgqkdnggdlvetaflm qgllavhqyyaegsaeekklagridklwrevdwnwyrhggqnvlywhwspeygwemnfpvhgyneclim yilaaaspthgvpaavyhegwaqngaivsphkvegielhlryqggeagplfwaqysflgldpvglkdey cpsyfnemrnltlvnreycirnpkhykgygpdcwgltasysvdgyaahgplerddrgvisptaalssiv ytpdqslqvmhhlyemgdkvfgpygfydafsetadwypkrylaidqgpiavmienyrtgllwklfmshp dvqnglkklgfnvkk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.12 Rfree 0.213
    Matthews' coefficent 2.35 Rfactor 0.158
    Waters 1248 Solvent Content 47.69

    Ligand Information


    Google Scholar output for 3eu8
    1. Functional classification of protein 3D structures from predicted local interaction sites
    R Parasuram, JS Lee, P Yin, S Somarowthu - J Bioinform Comput , 2010 - worldscinet.com

    Protein Summary

    390129 is a member of COG5368 family (NB: the family has changed from DUF239 to Glucoamylase, PF03080). The structure (Figure 1) has a alpha/alpha toroid fold and is similar to 1ayx (Z=19.9), 1glm (Z=19.4), 1gah, 1dog, 1agm, 3gly etc. The sequence similarities between 390129 and these structural homologs are usually less than 10%. Most of these structural homologs are glucoamylases which are involved in breaking down complex sugars (e.g. starch). The biological relevant state is likely monomeric. The putative active site is located at the center of the toroid with a well defined large cavity (Figure 2).


    Figure 1. The monomer of 390129


    Figure 2. The putative active site on the surface 390129


    Ligand Summary




    No references found.

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    Files (2)

    FileSizeDateAttached by 
    A monomer of 390129
    109.92 kB20:59, 2 Sep 2008qxuActions
    The surface of 390129 with the active site cavity
    150.44 kB20:59, 2 Sep 2008qxuActions
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