1y8e: Difference between revisions

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OCA, Eric Martz

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-{{Seed}}
+<table cellpadding='5'><tr><td style='background-color: yellow;border:2px solid black;font-size:150%;'>
-{{Template:Murthy_fraud}}
+WARNING: This structure was flagged as problematic. For additional information see '''2009, December:''' at [[Retractions and Fraud]].</td></tr></table>
-[[Image:1y8e.png|left|200px]]
+==VCP:Suramin Complex==
+<StructureSection load='1y8e' size='340' side='right' caption='[[1y8e]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1y8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y8E FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1g44|1g44]], [[1rid|1rid]]</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y8e RCSB], [http://www.ebi.ac.uk/pdbsum/1y8e PDBsum]</span></td></tr>
+</table>
+== 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/y8/1y8e_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/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Suramin is a competitive inhibitor of heparin binding to many proteins, including viral envelope proteins, protein tyrosine phosphatases, and fibroblast growth factors (FGFs). It has been clinically evaluated as a potential therapeutic in treatment of cancers caused by unregulated angiogenesis, triggered by FGFs. Although it has shown clinical promise in treatment of several cancers, suramin has many undesirable side effects. There is currently no experimental structure that reveals the molecular interactions responsible for suramin inhibition of heparin binding, which could be of potential use in structure-assisted design of improved analogues of suramin. We report the structure of suramin, in complex with the heparin-binding site of vaccinia virus complement control protein (VCP), which interacts with heparin in a geometrically similar manner to many FGFs. The larger than anticipated flexibility of suramin manifested in this structure, and other details of VCP-suramin interactions, might provide useful structural information for interpreting interactions of suramin with many proteins.
-<!--
+Structural basis for antagonism by suramin of heparin binding to vaccinia complement protein.,Ganesh VK, Muthuvel SK, Smith SA, Kotwal GJ, Murthy KH Biochemistry. 2005 Aug 16;44(32):10757-65. PMID:16086578<ref>PMID:16086578</ref>
-The line below this paragraph, containing "STRUCTURE_1y8e", 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_1y8e|  PDB=1y8e  |  SCENE=  }}
-===VCP:Suramin Complex===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+==See Also==
-<!--
+*[[Retractions and Fraud|Retractions and Fraud]]
-The line below this paragraph, {{ABSTRACT_PUBMED_16086578}}, adds the Publication Abstract to the page
+== References ==
-(as it appears on PubMed at http://www.pubmed.gov), where 16086578 is the PubMed ID number.
+<references/>
--->
+__TOC__
-{{ABSTRACT_PUBMED_16086578}}
+</StructureSection>
-==About this Structure==
-Y8E is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8E OCA].
-==Reference==
-<ref group="xtra">PMID:16086578</ref><references group="xtra"/>
 [[Category: Vaccinia virus]]
-[[Category: Ganesh, V K.]]
+[[Category: Ganesh, V K]]
-[[Category: Kotwal, G J.]]
+[[Category: Kotwal, G J]]
-[[Category: Murthy, K H.]]
+[[Category: Murthy, K H]]
-[[Category: Muthuvel, S K.]]
+[[Category: Muthuvel, S K]]
-[[Category: Smith, S A.]]
+[[Category: Smith, S A]]
 [[Category: Beta barrel]]
+[[Category: Viral protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:45:58 2009''