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The Open Protein Structure Annotation Network
PDB Keyword
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4ote

    Title Crystal structure of a putative lipoprotein (CD630_1653) from Clostridium difficile 630 at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 4ote Target Id 418088
    Molecular Characteristics
    Source Clostridium difficile 630
    Alias Ids TPS82153,YP_001088154.1, 323124 Molecular Weight 26530.07 Da.
    Residues 240 Isoelectric Point 5.47
    Sequence kddkkivvgatlvpggelleelkplikekgytlevknfddyilpnealnngeidanlfqhepylkeavk akgykimagkklyvcpailysykiksvdefkkgdtiaisnnpsscsknlrylesiglltlpkgdglvsp kdiienpkgiqfkeldiaqipsslpdvtaafidttyavpagldakkngiytapindeyanllafrtedk dsekikvlqdvltsdkarslieekykgiviptf
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.20 Rfree 0.2404
    Matthews' coefficent 2.73 Rfactor 0.1965
    Waters 211 Solvent Content 55.01

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    The protein YP_001088154.1 is annotated as putative lipoprotein. YP_001088154.1 belongs to PFAM PF03180 Lipoprotein_9.

     

    The monomer structure is shown below. There is a SelenoMet amino acid (shown in sticks) bound in the putative active site of each chain.

    SP17422AN_mon.png

    A zoomed-in view of the putative active site is shown below.

    SP17422AN_lig.png

    Top 10 DALI Structural Homologs
     
    N PDB Z-score RMSD LALI NRES %ID Description (JCSG structures highlighted in red)
    1 4k3f 31.4 1.6 235 241 36 Probable Tonb-dependent Receptor
    2 4ib2 30.3 1.8 235 244 33 Putative Lipoprotein
    3 4got 30.2 1.7 236 248 39 Methionine-binding Lipoprotein Metq
    4 4ef2 30.0 1.8 234 242 37 Pheromone Cob1/lipoprotein, Yaec Family
    5 4ef1 30.0 1.8 235 246 37 Pheromone Cob1/lipoprotein, Yaec Family
    6 3up9 29.9 2.0 233 240 31 Putative Uncharacterized Protein
    7 3tqw 29.2 1.6 229 234 37 Methionine-binding Protein
    8 1xs5 28.7 1.9 233 240 27 Membrane Lipoprotein Tpn32
    9 3ir1 28.3 1.8 234 240 33 Outer Membrane Lipoprotein Gna1946
    10 3gxa 28.3 1.8 234 240 34 Outer Membrane Lipoprotein Gna1946

     

    The superposition of YP_001088154.1 (green) on 4k3f (magenta) is shown below. Both these proteins have bound SelenoMet.

    SP17422AN_4k3f.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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