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3p94

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

    Title Crystal structure of a GDSL-like Lipase (BDI_0976) from Parabacteroides distasonis ATCC 8503 at 1.93 A resolution. To be published
    Site JCSG
    PDB Id 3p94 Target Id 406137
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS31051,YP_001302366.1, 322626 Molecular Weight 22764.03 Da.
    Residues 203 Isoelectric Point 8.58
    Sequence ekgdwaqfgryaeanktvkvpsnvvfmgnsitdgwwpadstffirnnfvdrgisgqttsemlvrfrqdv inlkpkavvilagindiahnngvialenvfgnlvsmaelakanhikvifcsvlpaydfpwrpgmqpadk viqlnkwikeyadkngltyvdyhsamkdernglpanlskdgvhptlegykimekivleaihktvk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.93 Rfree 0.207
    Matthews' coefficent 2.24 Rfactor 0.183
    Waters 721 Solvent Content 45.12

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Gene BDI_0976 from Parabacteroides distasonis atcc 8503 encodes for a GDSL lipase (PFAM family PFAM:PF00657), homologous to platelet activating factors (PDB:2hsj, PDB:1es9, PDB:1wab, etc). This could be interesting as the bacteria producing this protein is from a symbiont of human. Other structures from the GDSL family solved by the JCSG are PDB:1z8h and PDB:1vjg.

     Dali hits:

         1:  2hsj-A 23.3  2.6  193   211   21 PDB  MOLECULE: PUTATIVE PLATELET ACTIVATING FACTOR;                       
       2:  2hsj-D 23.2  2.6  193   214   21 PDB  MOLECULE: PUTATIVE PLATELET ACTIVATING FACTOR;                       
       3:  2hsj-B 23.2  2.6  193   212   21 PDB  MOLECULE: PUTATIVE PLATELET ACTIVATING FACTOR;                       
       4:  2hsj-C 23.2  2.6  193   212   21 PDB  MOLECULE: PUTATIVE PLATELET ACTIVATING FACTOR;                       
       5:  1es9-A 22.3  2.6  187   212   19 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
       6:  1wab-A 22.3  2.6  187   212   19 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE;                
       7:  1bwq-A 22.3  2.6  187   212   19 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE;                
       8:  3dt9-A 22.2  2.6  187   212   19 PDB  MOLECULE: BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE           
       9:  3dt8-A 22.1  2.6  187   212   19 PDB  MOLECULE: BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE           
      10:  3dt6-A 22.1  2.6  187   212   19 PDB  MOLECULE: BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE           
      11:  1bwr-A 22.0  2.6  187   212   19 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE;                
      12:  1bwp-A 22.0  2.6  187   212   19 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE;                
      13:  1fxw-A 21.7  2.7  186   211   19 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      14:  1fxw-F 21.5  2.6  187   212   24 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      15:  1vyh-B 21.3  2.7  188   218   23 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      16:  1vyh-Q 21.3  2.7  188   218   23 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      17:  1vyh-J 21.3  2.7  188   218   23 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      18:  1vyh-R 21.3  2.7  188   218   23 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      19:  1vyh-M 21.3  2.7  188   218   23 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      20:  1vyh-E 21.3  2.7  188   218   23 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      21:  1vyh-F 21.3  2.7  188   218   23 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      22:  1vyh-N 21.3  2.7  188   218   23 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      23:  1vyh-A 21.2  2.7  188   218   23 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      24:  1vyh-I 21.2  2.7  188   218   23 PDB  MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB              
      25:  1yzf-A 20.6  2.3  171   195   25 PDB  MOLECULE: LIPASE/ACYLHYDROLASE;                                      
      26:  2q0s-E 19.6  2.1  168   215   17 PDB  MOLECULE: ARYL ESTERASE;  

     

    Fig. 1. monomer with highlighted catalytic triad (S54,D202,H205)

    tt4069a.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (1)

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     tt4069a.png
    tt4069a monomer
    143.79 kB21:48, 5 Oct 2010qxuActions
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