1ijl: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1ijl.jpg|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_1ijl", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_1ijl|  PDB=1ijl  |  SCENE=  }}
'''Crystal structure of acidic phospholipase A2 from deinagkistrodon acutus'''


==Crystal structure of acidic phospholipase A2 from deinagkistrodon acutus==
<StructureSection load='1ijl' size='340' side='right'caption='[[1ijl]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ijl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinagkistrodon_acutus Deinagkistrodon acutus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IJL FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ijl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ijl OCA], [https://pdbe.org/1ijl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ijl RCSB], [https://www.ebi.ac.uk/pdbsum/1ijl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ijl ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PA2A_DEIAC PA2A_DEIAC] Snake venom phospholipase A2 (PLA2) that inhibits ADP-induced platelet aggregation. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:8931260</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ij/1ijl_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ijl ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
An acidic phospholipase A(2) was purified from Deinagkistrodon acutus (Agkistrodon acutus) which displays an inhibitory effect on platelet aggregation. The three-dimensional structure of the enzyme was determined by molecular replacement at 2.6 A resolution with a crystallographic R factor of 18.40% (R(free) = 22.50%) and reasonable stereochemistry. Two molecules in the asymmetric unit form a dimer and the dimer formation accompanies a significant conformational adaptation of segment 14-23, a constituent of the 'interface recognition site' (IRS). This probably reflects the inherent structural flexibility of the IRS. The possible expansion of the site for inhibiting platelet aggregation as proposed previously [Wang et al. (1996), J. Mol. Biol. 255, 669-676] is discussed.


==Overview==
Structure of an acidic phospholipase A2 from the venom of Deinagkistrodon acutus.,Gu L, Zhang H, Song S, Zhou Y, Lin Z Acta Crystallogr D Biol Crystallogr. 2002 Jan;58(Pt 1):104-10. Epub 2001, Dec 21. PMID:11752784<ref>PMID:11752784</ref>
An acidic phospholipase A(2) was purified from Deinagkistrodon acutus (Agkistrodon acutus) which displays an inhibitory effect on platelet aggregation. The three-dimensional structure of the enzyme was determined by molecular replacement at 2.6 A resolution with a crystallographic R factor of 18.40% (R(free) = 22.50%) and reasonable stereochemistry. Two molecules in the asymmetric unit form a dimer and the dimer formation accompanies a significant conformational adaptation of segment 14-23, a constituent of the 'interface recognition site' (IRS). This probably reflects the inherent structural flexibility of the IRS. The possible expansion of the site for inhibiting platelet aggregation as proposed previously [Wang et al. (1996), J. Mol. Biol. 255, 669-676] is discussed.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1IJL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Deinagkistrodon_acutus Deinagkistrodon acutus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IJL OCA].
</div>
<div class="pdbe-citations 1ijl" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Structure of an acidic phospholipase A2 from the venom of Deinagkistrodon acutus., Gu L, Zhang H, Song S, Zhou Y, Lin Z, Acta Crystallogr D Biol Crystallogr. 2002 Jan;58(Pt 1):104-10. Epub 2001, Dec 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11752784 11752784]
*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Deinagkistrodon acutus]]
[[Category: Deinagkistrodon acutus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Gu, L.]]
[[Category: Gu L]]
[[Category: Lin, Z.]]
[[Category: Lin Z]]
[[Category: Song, S.]]
[[Category: Song S]]
[[Category: Zhang, H.]]
[[Category: Zhang H]]
[[Category: Zhou, Y.]]
[[Category: Zhou Y]]
[[Category: Calcium binding loop]]
[[Category: One two strand beta sheet]]
[[Category: Three long helix]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 20:04:28 2008''
Retrieved from "https://proteopedia.org/1ijl"