1bk9: Difference between revisions
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< | ==PHOSPHOLIPASE A2 MODIFIED BY PBPB== | ||
<StructureSection load='1bk9' size='340' side='right'caption='[[1bk9]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1bk9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gloydius_halys Gloydius halys]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BK9 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]] 2Å</td></tr> | |||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PBP:1-(4-BROMO-PHENYL)-ETHANONE'>PBP</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=1bk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bk9 OCA], [https://pdbe.org/1bk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bk9 RCSB], [https://www.ebi.ac.uk/pdbsum/1bk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bk9 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PA2A_GLOHA PA2A_GLOHA] Snake venom phospholipase A2 (PLA2) that acts in vivo as an anti-thrombotic agent. Inhibits platelet aggregation induced by ADP, arachidonic acid, and thrombin. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:18456297</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/bk/1bk9_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=1bk9 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The crystal structure of acidic phospholipase A2 (APLA2) from Agkistrodon halys pallas covalently modified by p-bromo-phenacyl-bromide (pBPB) was determined to a resolution of 2.0 A by an isomorphous difference Fourier method with the native APLA2 structure as an initial model and refined to a crystallographic R factor of 15.3%. The modified APLA2 structure is remarkably similar to that of the native one. Least-squares superposition of C alpha atoms of native and modified APLA2 results in a root-mean-square coordinate deviation of 0.243 A. The p-bromo-phenacyl group near the active site occupies a position similar to that in pBPB modified bovine pancreatic PLA2. The inhibitor covalently bound to the NDI atom of His48 fits well in the hydrophobic channel, forming extensive hydrophobic interactions with the surrounding residues, especially with the side chains of Phe5 and Cys45 and the main chain of Gly30. However, the inhibitor does not change the conformation of these residues except that Trp31 at the entrance of the hydrophobic channel moves slightly toward the inhibitor. Compared with native APLA2, the Ca2+-binding loop shows a little conformational change and a cation, probably Na+, occupies in the position of Ca2+. The binding of pBPB to APLA2 induce no other significant conformational changes in the enzyme molecule elsewhere. | |||
Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide.,Zhao H, Tang L, Wang X, Zhou Y, Lin Z Toxicon. 1998 Jun;36(6):875-86. PMID:9663694<ref>PMID:9663694</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1bk9" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
[[Category: Gloydius halys]] | [[Category: Gloydius halys]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Lin | [[Category: Lin Z]] | ||
[[Category: Tang | [[Category: Tang L]] | ||
[[Category: Wang | [[Category: Wang X]] | ||
[[Category: Zhao | [[Category: Zhao H]] | ||
[[Category: Zhou | [[Category: Zhou Y]] | ||
Latest revision as of 10:12, 9 October 2024
PHOSPHOLIPASE A2 MODIFIED BY PBPBPHOSPHOLIPASE A2 MODIFIED BY PBPB
Structural highlights
FunctionPA2A_GLOHA Snake venom phospholipase A2 (PLA2) that acts in vivo as an anti-thrombotic agent. Inhibits platelet aggregation induced by ADP, arachidonic acid, and thrombin. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.[1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe crystal structure of acidic phospholipase A2 (APLA2) from Agkistrodon halys pallas covalently modified by p-bromo-phenacyl-bromide (pBPB) was determined to a resolution of 2.0 A by an isomorphous difference Fourier method with the native APLA2 structure as an initial model and refined to a crystallographic R factor of 15.3%. The modified APLA2 structure is remarkably similar to that of the native one. Least-squares superposition of C alpha atoms of native and modified APLA2 results in a root-mean-square coordinate deviation of 0.243 A. The p-bromo-phenacyl group near the active site occupies a position similar to that in pBPB modified bovine pancreatic PLA2. The inhibitor covalently bound to the NDI atom of His48 fits well in the hydrophobic channel, forming extensive hydrophobic interactions with the surrounding residues, especially with the side chains of Phe5 and Cys45 and the main chain of Gly30. However, the inhibitor does not change the conformation of these residues except that Trp31 at the entrance of the hydrophobic channel moves slightly toward the inhibitor. Compared with native APLA2, the Ca2+-binding loop shows a little conformational change and a cation, probably Na+, occupies in the position of Ca2+. The binding of pBPB to APLA2 induce no other significant conformational changes in the enzyme molecule elsewhere. Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide.,Zhao H, Tang L, Wang X, Zhou Y, Lin Z Toxicon. 1998 Jun;36(6):875-86. PMID:9663694[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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