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The Open Protein Structure Annotation Network
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3ddd

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of A Putative Acetyltransferase (NP_142035.1) from PYROCOCCUS HORIKOSHII at 2.25 A resolution. To be published
    Site JCSG
    PDB Id 3ddd Target Id 379751
    Molecular Characteristics
    Source Pyrococcus horikoshii ot3
    Alias Ids TPS7216,NP_142035.1, 103975 Molecular Weight 30841.50 Da.
    Residues 269 Isoelectric Point 9.25
    Sequence miiryatpddiedmvsifidaynfpgpresvkssfeislevqpdgcllaflkdepvgmgciffynkqaw iglmgvkkayqrrgigtevfrrlleigrrkvdtirldassqgyglykkfkfvdeyrtvryelmerpikr vegvvevnkipnwvkeidkkafgddrirvleaymrrgarllcaenegfglvyrgkigplvadsprvaek illkafqlgareiiipevnkdalelikifkpsqvtscmrmrlgskieekvdiyygilayakg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.25 Rfree 0.221
    Matthews' coefficent 3.40 Rfactor 0.168
    Waters 175 Solvent Content 63.81

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ddd
    1. Antigen binding proteins to proprotein convertase subtilisin kexin type 9 (PCSK9)
    SM Jackson, B Shan, W Shen, CT King - US Patent 8,030,457, 2011 - Google Patents
     

    Protein Summary

    379751 shares sequence similarity with the Acetyltransferase (GNAT) family from Pfam (E-value: 1.1e-13). It is likely a monomer, as suggested by crystal packing and size exclusion chromatography. 379751 contains one CoA monomer shown as stick in the presumable active site. 

    379751 also has sequence similarity to a putative acetyltransferase of GNAT family from Shigella flexneri (PDB code: 2pdo, FFAS score: -48.600), which also has a topsan page, and a yeast GNA1 (PDB code: 1i1d, FFAS score: -44.100). The superposition of 379751 and 1i1d indicates that N-terminal of 379751 fits well (green: 379751; 269 aa, cyan: 1i1d; 159aa). 


    The superposition of the CoA binding region in between 379751 and 1i1d is shown below. (green: 379751, cyan: 1i1d). 379751 contains CoA while 1i1d contains CoA and N-acetyl-D-glycosamine-6-phosphate. The conserved residues (Val75, Gly85 and Tyr115 of 379751,  and Val102, Gly112 and Tyr143 of 1i1d) are shown as stick.  Based on the sequence and structure similarity, 379751 is a putative acetyltransferase from the GNAT family.


    Ligand Summary

    - One CoA monomer is modeled based on the presence of clear and conclusive electron density.
    - EDO molecules from cryo condition were modeled.

    Reviews

    References

     

    No references found.

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