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The Open Protein Structure Annotation Network
PDB Keyword
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3imm

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

    Title Crystal structure of Putative glycosyl hydrolase (YP_001301887.1) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3imm Target Id 385843
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25706,YP_001301887.1 Molecular Weight 22556.42 Da.
    Residues 200 Isoelectric Point 5.76
    Sequence adnnkwkplfgknlenanynpevwsetdgvlgavkdesiwtkdeyenfeldldfktdvgtnsgvvvyct dtkdwipnsveiqiaddhcekwgngkpyekcgaiyghlgavqdkvvkkpgewnhmrikcagqhimviln gkkvtemdmskwtsgtknpdgsdipswlpkpfaelptkgfiglqgkhgdsliwfrnikirsl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 2.00 Rfree 0.222
    Matthews' coefficent 2.09 Rfactor 0.163
    Waters 395 Solvent Content 41.27

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3imm
    1. Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement
    A Roy, Y Zhang - Structure, 2012 - Elsevier
     

    Protein Summary

     

    Target id 385843 belongs to Pfam group DUF1080 (PF06439) and is classified in Pfam as a domain of unknown function. This protein is now in family PF06439.4 DUF1080 CL0004, and is probably a glycosyl hydrolase. There are other structures in the family.

     

     C.png

    In the crystallographic asymmetric unit, three protomers are found. However, the biological molecule is a monomer.

     ABC.png

    The structure of 385843 is very flexible. Most of the residues are involved in loops (56.9%), and beta-strands (37.6%), 3-10 helix (5.6%) and no alpha helix (0.0%) found. Besides that, most side chains and even some of main chains are different between three protomers. In the putative active site, a Tris molecule is found in the protomer C and a Na ion is found in the protomer B. A protomer contains waters only in the putative active site.

     

    The 385843 structure is similar to the recent JSCG structure, 3h3l (topsan_page, rmsd=2.3A, 187 Ca aligned, 24% id). However,  385843 (green) seems to be more flexible containing many loops comparing to 3h3l (light blue) as shown below.

     

    super_3h3l.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (3)

    FileSizeDateAttached by 
     ABC.png
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    202.35 kB02:38, 21 May 2009gyewonActions
     C.png
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    175.63 kB02:20, 21 May 2009gyewonActions
     super_3h3l.png
    No description
    262.06 kB02:20, 21 May 2009gyewonActions
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