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The Open Protein Structure Annotation Network
PDB Keyword
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3r8e

    Title Crystal structure of a Hypothetical sugar kinase (CHU_1875) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.65 A resolution. To be published
    Site JCSG
    PDB Id 3r8e Target Id 394547
    Molecular Characteristics
    Source Cytophaga hutchinsonii atcc 33406
    Alias Ids TPS27877,YP_678483.1, _0120.002476_, 325469 Molecular Weight 32417.98 Da.
    Residues 302 Isoelectric Point 5.61
    Sequence milgidvggtsvkfglvtpegeiqnatrfmtadwvngigfvesmkleignflkqypivkgvgigwpglv sldrtkvillpnipsvvnvpiveilrsefphihfkiendakcaalgeyyfgenkrmqtfillalgtgvg sgvmmngklfiggrgngtevghmlttrgkslenqvginhliaytheqlaldvakksslhtiaelspkvi adhaaqgdalalavwadigtiigeslvnivrvmdlnnillgggisgafdyfvpnlkkamlehlptyytd dmyigkatlendagllgaaglimeai
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.65 Rfree 0.2346
    Matthews' coefficent 2.62 Rfactor 0.2137
    Waters 212 Solvent Content 53.03

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3r8e

    Protein Summary

    The protein YP_678483.1 is annotated as a glucokinase. YP_678483.1 belongs to PFAM PF00480 ROK.

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    Note from PFAM:

    This sequence appears to have a ROK (PF00480) domain on it for the first 176 residues and then a BcrAD_BadFG (BadF/BadG/BcrA/BcrD ATPase family) just below threshold at the C-terminus. Both of these families are in the Actin-like ATPase Superfamily clan CL0108. Both these families have other structures.

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    The monomer structure is shown below in rainbow and secondary-structure representations.

    MH15473A_mon.png MH15473A_ss.png

     

    Three regions of the structure (residues 8-12, 27-51, and 66-101) are poorly ordered and therefore have been modeled in two conformations. These regions have been shown below in orange, yellow and magenta colors.

    MH15473A_disordered.png

     

    The protein should form a dimer as shown below.

    MH15473A_dimer.png

     

    The homologs of this structure are listed below.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID Description (JCSG structures highlighted in red)
    1 2qm1 30.0 2.4 269 325 30 Glucokinase
    2 1z05 26.8 2.2 267 396 24 Transcriptional Regulator, Rok Family
    3 3eo3 26.6 2.5 248 288 24 Bifunctional Udp-n-acetylglucosamine 2-
    4 3epq 26.5 2.2 238 294 24 Putative Fructokinase
    5 3lm9 26.4 2.3 238 294 25 Fructokinase
    6 1xc3 26.4 2.3 239 295 25 Putative Fructokinase
    7 1z6r 26.3 2.2 265 382 19 Mlc Protein
    8 2gup 26.2 2.7 253 289 27 Rok Family Protein
    9 2aa4 25.8 2.8 246 289 24 Putative N-acetylmannosamine Kinase
    10 2hoe 25.6 2.7 247 354 22 N-acetylglucosamine Kinase

    Ligand Summary

    Reviews

    References

     

    No references found.

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