1qe2 - Revision history

OCA at 09:54, 15 September 2021

OCA — Wed, 15 Sep 2021 09:54:52 GMT

←Older revision		Revision as of 09:54, 15 September 2021
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	<StructureSection load='1qe2' size='340' side='right'caption='[[1qe2]]' scene=''>		<StructureSection load='1qe2' size='340' side='right'caption='[[1qe2]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1QE2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QE2 FirstGlance]. <br>
-	</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=1qe2 FirstGlance], [~~http~~://www.ebi.ac.uk/pdbsum/1qe2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qe2 ProSAT]</span></td></tr>	+	</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=1qe2 FirstGlance], [https://www.ebi.ac.uk/pdbsum/1qe2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qe2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:16, 27 November 2019

OCA — Wed, 27 Nov 2019 10:16:43 GMT

←Older revision		Revision as of 10:16, 27 November 2019
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	==THEORETICAL SUBSTRATE-FREE ZINC-BOUND FARNESYLTRANSFERASE GENERATED BY MOLECULAR DYNAMICS SIMULATIONS==		==THEORETICAL SUBSTRATE-FREE ZINC-BOUND FARNESYLTRANSFERASE GENERATED BY MOLECULAR DYNAMICS SIMULATIONS==
-	<StructureSection load='1qe2' size='340' side='right' caption='[[1qe2]]' scene=''>	+	<StructureSection load='1qe2' size='340' side='right'caption='[[1qe2]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QE2 FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QE2 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Theoretical Model]]		[[Category: Theoretical Model]]
		+	[[Category: Large Structures]]
	[[Category: Pang, Y P]]		[[Category: Pang, Y P]]
	[[Category: Prendergast, F G]]		[[Category: Prendergast, F G]]
	[[Category: Xu, K]]		[[Category: Xu, K]]

OCA at 08:16, 24 February 2018

OCA — Sat, 24 Feb 2018 08:16:18 GMT

←Older revision		Revision as of 08:16, 24 February 2018
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QE2 FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QE2 FirstGlance]. <br>
-	</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=1qe2 FirstGlance], [http://www.ebi.ac.uk/pdbsum/1qe2 PDBsum]</span></td></tr>	+	</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=1qe2 FirstGlance], [http://www.ebi.ac.uk/pdbsum/1qe2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qe2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:44, 11 February 2016

OCA — Thu, 11 Feb 2016 09:44:02 GMT

←Older revision		Revision as of 09:44, 11 February 2016
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		+	{{Theoretical_model}}
		+
	==THEORETICAL SUBSTRATE-FREE ZINC-BOUND FARNESYLTRANSFERASE GENERATED BY MOLECULAR DYNAMICS SIMULATIONS==		==THEORETICAL SUBSTRATE-FREE ZINC-BOUND FARNESYLTRANSFERASE GENERATED BY MOLECULAR DYNAMICS SIMULATIONS==
	<StructureSection load='1qe2' size='340' side='right' caption='[[1qe2]]' scene=''>		<StructureSection load='1qe2' size='340' side='right' caption='[[1qe2]]' scene=''>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Theoretical Model]]
	[[Category: Pang, Y P]]		[[Category: Pang, Y P]]
	[[Category: Prendergast, F G]]		[[Category: Prendergast, F G]]
	[[Category: Xu, K]]		[[Category: Xu, K]]

OCA at 17:59, 10 September 2015

OCA — Thu, 10 Sep 2015 17:59:31 GMT

←Older revision		Revision as of 17:59, 10 September 2015
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1qe2" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:13, 6 January 2015

OCA — Tue, 06 Jan 2015 07:13:50 GMT

←Older revision		Revision as of 07:13, 6 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QE2 FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QE2 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qe2 FirstGlance], [http://www.ebi.ac.uk/pdbsum/1qe2 PDBsum]</span></td></tr>	+	</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=1qe2 FirstGlance], [http://www.ebi.ac.uk/pdbsum/1qe2 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 21:10, 28 September 2014

OCA — Sun, 28 Sep 2014 21:10:32 GMT

←Older revision		Revision as of 21:10, 28 September 2014
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-	~~{{Theoretical_model}}~~	+	==THEORETICAL SUBSTRATE-FREE ZINC-BOUND FARNESYLTRANSFERASE GENERATED BY MOLECULAR DYNAMICS SIMULATIONS==
		+	<StructureSection load='1qe2' size='340' side='right' caption='[[1qe2]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QE2 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qe2 FirstGlance], [http://www.ebi.ac.uk/pdbsum/1qe2 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Farnesyltransferase (FT) inhibitors can suppress tumor cell proliferation without substantially interfering with normal cell growth, thus holding promise for cancer treatment. A structure-based approach to the design of improved FT inhibitors relies on knowledge of the conformational flexibility of the zinc-containing active site of FT. Although several X-ray structures of FT have been reported, detailed information regarding the active site conformational flexibility of the enzyme is still not available. Molecular dynamics (MD) simulations of FT can offer the requisite information, but have not been applied due to a lack of effective methods for simulating the four-ligand coordination of zinc in proteins. Here, we report in detail the problems that occurred in the conventional MD simulations of the zinc-bound FT and a solution to these problems by employing a simple method that uses cationic dummy atoms to impose orientational requirement for zinc ligands. A successful 1.0 ns (1.0 fs time step) MD simulation of zinc-bound FT suggests that nine conserved residues (Asn127alpha, Gln162alpha, Asn165alpha, Gln195alpha, His248beta, Lys294beta, Leu295beta, Lys353beta, and Ser357beta) in the active site of mammalian FT are relatively mobile. Some of these residues might be involved in the ligand-induced active site conformational rearrangement upon binding and deserve attention in screening and design of improved FT inhibitors for cancer chemotherapy.

-	~~[[Image~~:~~1qe2~~.~~png\|left\|200px]]~~	+	Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach.,Pang YP, Xu K, Yazal JE, Prendergas FG Protein Sci. 2000 Oct;9(10):1857-65. PMID:11106157<ref>PMID:11106157</ref>

-	~~{{STRUCTURE_1qe2\| PDB=1qe2 \| SCENE= }}~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	==~~=THEORETICAL SUBSTRATE-FREE ZINC-BOUND FARNESYLTRANSFERASE GENERATED BY MOLECULAR DYNAMICS SIMULATIONS===~~	+	== References ==
-		+	<references/>
-	~~{{ABSTRACT_PUBMED_11106157}}~~	+	__TOC__
-		+	</StructureSection>
-	~~==Reference~~==	+
-	<~~ref group="xtra">PMID:011106157<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pang, Y P]]		[[Category: Pang, Y P]]
	[[Category: Prendergast, F G]]		[[Category: Prendergast, F G]]
	[[Category: Xu, K]]		[[Category: Xu, K]]

OCA: Protected "1qe2" [edit=sysop:move=sysop]

OCA — Sun, 21 Oct 2012 09:07:03 GMT

Protected "1qe2" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:07, 21 October 2012

OCA at 09:07, 21 October 2012

OCA — Sun, 21 Oct 2012 09:07:00 GMT

←Older revision		Revision as of 09:07, 21 October 2012
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	{{Theoretical_model}}		{{Theoretical_model}}
-	~~{{Seed}}~~	+
	[[Image:1qe2.png\|left\|200px]]		[[Image:1qe2.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1qe2", 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),
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-	-->
	{{STRUCTURE_1qe2\| PDB=1qe2 \| SCENE= }}		{{STRUCTURE_1qe2\| PDB=1qe2 \| SCENE= }}

	===THEORETICAL SUBSTRATE-FREE ZINC-BOUND FARNESYLTRANSFERASE GENERATED BY MOLECULAR DYNAMICS SIMULATIONS===		===THEORETICAL SUBSTRATE-FREE ZINC-BOUND FARNESYLTRANSFERASE GENERATED BY MOLECULAR DYNAMICS SIMULATIONS===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11106157}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11106157 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11106157}}		{{ABSTRACT_PUBMED_11106157}}
-
-	==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QE2 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11106157~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011106157</ref><references group="xtra"/>
	[[Category: Pang, Y P]]		[[Category: Pang, Y P]]
	[[Category: Prendergast, F G]]		[[Category: Prendergast, F G]]
	[[Category: Xu, K]]		[[Category: Xu, K]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 8 07:42:38 2010''

OCA at 04:42, 8 April 2010

OCA — Thu, 08 Apr 2010 04:42:38 GMT

←Older revision		Revision as of 04:42, 8 April 2010
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-	~~'''Theoretical Model'''~~	+	{{Theoretical_model}}
		+	{{Seed}}
		+	[[Image:1qe2.png\|left\|200px]]

-	The ~~entry 1QE2~~ is ~~a Theoretical Model titled 'THEORETICAL SUBSTRATE~~-~~FREE ZINC~~-~~BOUND FARNESYLTRANSFERASE GENERATED BY MOLECULAR DYNAMICS SIMULATIONS'.~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_1qe2", 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_1qe2\| PDB=1qe2 \| SCENE= }}

-	~~[[Category:Theoretical Model]]~~	+	===THEORETICAL SUBSTRATE-FREE ZINC-BOUND FARNESYLTRANSFERASE GENERATED BY MOLECULAR DYNAMICS SIMULATIONS===


-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 30 09~~:52:~~54 2008~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_11106157}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 11106157 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_11106157}}
		+
		+	==About this Structure==
		+	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QE2 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:11106157</ref><references group="xtra"/>
		+	[[Category: Pang, Y P]]
		+	[[Category: Prendergast, F G]]
		+	[[Category: Xu, K]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 8 07:42:38 2010''