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 Periplasmic Binding Protein BMA293 (YP_104442.1) from Burkholderia mallei ATCC 23344 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3i09 Target Id 396165
    Molecular Characteristics
    Source Burkholderia mallei atcc 23344
    Alias Ids TPS25855,YP_104442.1, BIG_798, 332887 Molecular Weight 40614.19 Da.
    Residues 374 Isoelectric Point 8.69
    Sequence adsvkigfitdmsglyadidgqggleaikmavadfggkvngkpievvyadhqnkadiaaskarewmdrg gldllvggtnsatalsmnqvaaekkkvyinigagadtltneqctpytvhyaydtmalakgtgsavvkqg gktwffltadyafgkalekntadvvkanggkvlgevrhplsasdfssfllqaqsskaqilglanaggdt vnaikaakefgitktmklaallmfindvhalglettqglvltdswywnrdqasrqwaqryfakmkkmps slqaadyssvttylkavqaagstdsdkvmaqlkkmkiddfyakgyirtdgsmihdmylmevkkpseske pwdyykvvatipgeqafttkqetrcalwk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.80 Rfree 0.174
    Matthews' coefficent 2.11 Rfactor 0.137
    Waters 723 Solvent Content 41.73

    Ligand Information


    Google Scholar output for 3i09

    Protein Summary

    Gene BMA2936 from Burkholderia mallei atcc 23344 encodes the YP_104442 protein belonging to the ANF receptor ligand binding group (PF01094). Based on its genome context, BMA2936 could be a periplasmic amino acid binding domain of an ABC transporter. This protein is now in family PF01094.21 ANF_receptor CL0144.

    Pre-SCOP classifies 3i09 in the alpha/beta class, periplasmic binding protein-like I superfamily, L-arabionse binding protein-like family. 3i09 structure is highly similar to 1pea with 86% of SSM and 1z17 with 83%. fastSCOP top hit is 1qo0 with an e-value of 1e-77, whereas Dali top Z-scores are 42.2 for 1pea and 41.5 for 1qo0. FATCAT scores 830 with 1qo0. All three structures consist of two domains that fold into a closed conformation upon ligand binding.


    Figure 1. 3i09 monomer structure




    The protein is annotated as a branched amino acid binding protein; however, an acetoacetic acid (AAE) is present in the active site. This protein lacks an acidic residue for interaction with the amino group of a free aa. Suggesting: 1). this is a branch aa binding domain but also it has affinity for AAE; 2). 3i09 binds AAE or similar ligands (but not branched aa).

    Figure 2. AAE and its interacting residues in 3i09 structure. The AAE is also shown in density (blue)


    Ligand Summary




    No references found.

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    Files (2)

    FileSizeDateAttached by 
    396165 monomer
    299.05 kB17:27, 27 Apr 2009qxuActions
    substrate binding site
    161.56 kB17:27, 27 Apr 2009qxuActions
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