3bjw

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:47, 1 November 2023) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3bjw.png|left|200px]]
 
-
<!--
+
==Crystal Structure of ecarpholin S complexed with suramin==
-
The line below this paragraph, containing "STRUCTURE_3bjw", creates the "Structure Box" on the page.
+
<StructureSection load='3bjw' size='340' side='right'caption='[[3bjw]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3bjw]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Echis_carinatus Echis carinatus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qhg 2qhg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BJW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BJW FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SVR:8,8-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC+ACID'>SVR</scene></td></tr>
-
{{STRUCTURE_3bjw| PDB=3bjw | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bjw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bjw OCA], [https://pdbe.org/3bjw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bjw RCSB], [https://www.ebi.ac.uk/pdbsum/3bjw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bjw ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PA2HS_ECHCA PA2HS_ECHCA]
 +
== 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/bj/3bjw_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3bjw ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Phospholipase A(2) (PLA(2)), a common toxic component of snake venom, has been implicated in various pharmacological effects. Ecarpholin S, isolated from the venom of the snake Echis carinatus sochureki, is a phospholipase A(2) (PLA(2)) belonging to the Ser(49)-PLA(2) subgroup. It has been characterized as having low enzymatic but potent myotoxic activities. The crystal structures of native ecarpholin S and its complexes with lauric acid, and its inhibitor suramin, were elucidated. This is the first report of the structure of a member of the Ser(49)-PLA(2) subgroup. We also examined interactions of ecarpholin S with phosphatidylglycerol and lauric acid, using surface plasmon resonance, and of suramin with isothermal titration calorimetry. Most Ca(2+)-dependent PLA(2) enzymes have Asp in position 49, which plays a crucial role in Ca(2+) binding. The three-dimensional structure of ecarpholin S reveals a unique conformation of the Ca(2+)-binding loop that is not favorable for Ca(2+) coordination. Furthermore, the endogenously bound fatty acid (lauric acid) in the hydrophobic channel may also interrupt the catalytic cycle. These two observations may account for the low enzymatic activity of ecarpholin S, despite full retention of the catalytic machinery. These observations may also be applicable to other non-Asp(49)-PLA(2) enzymes. The interaction of suramin in its complex with ecarpholin S is quite different from that reported for the Lys(49)-PLA(2)/suramin complex(,) where the interfacial recognition face (i-face), C-terminal region, and N-terminal region of ecarpholin S play important roles. This study provides significant structural and functional insights into the myotoxic activity of ecarpholin S and, in general, of non-Asp(49)-PLA(2) enzymes.
-
===Crystal Structure of ecarpholin S complexed with suramin===
+
Structural characterization of myotoxic ecarpholin S from Echis carinatus venom.,Zhou X, Tan TC, Valiyaveettil S, Go ML, Kini RM, Velazquez-Campoy A, Sivaraman J Biophys J. 2008 Oct;95(7):3366-80. Epub 2008 Jun 27. PMID:18586854<ref>PMID:18586854</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3bjw" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18586854}}, adds the Publication Abstract to the page
+
*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 18586854 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18586854}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
3BJW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Echis_carinatus Echis carinatus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qhg 2qhg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BJW OCA].
+
-
 
+
-
==Reference==
+
-
Structural characterization of myotoxic ecarpholin S from Echis carinatus venom., Zhou X, Tan TC, Valiyaveettil S, Go ML, Kini RM, Velazquez-Campoy A, Sivaraman J, Biophys J. 2008 Oct;95(7):3366-80. Epub 2008 Jun 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18586854 18586854]
+
[[Category: Echis carinatus]]
[[Category: Echis carinatus]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Sivaraman, J.]]
+
[[Category: Sivaraman J]]
-
[[Category: Zhou, X.]]
+
[[Category: Zhou X]]
-
[[Category: Calcium]]
+
-
[[Category: Complex]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Lipid degradation]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Phospholipase a2]]
+
-
[[Category: Secreted]]
+
-
[[Category: Ser49]]
+
-
[[Category: Snake venom]]
+
-
[[Category: Suramin]]
+
-
[[Category: Toxin]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 1 21:22:43 2008''
+

Current revision

Crystal Structure of ecarpholin S complexed with suramin

PDB ID 3bjw

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3bjw"
Personal tools