6l96 - Revision history

OCA at 10:53, 22 November 2023

OCA — Wed, 22 Nov 2023 10:53:28 GMT

←Older revision		Revision as of 10:53, 22 November 2023
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	<StructureSection load='6l96' size='340' side='right'caption='[[6l96]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='6l96' size='340' side='right'caption='[[6l96]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6l96]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L96 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6L96 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6l96]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L96 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L96 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=P7F:(2~{R})-2-[3-[[1,3-benzoxazol-2-yl-[3-(4-methoxyphenoxy)propyl]amino]methyl]phenoxy]butanoic+acid'>P7F</scene>~~</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.2Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPARA, NR1C1, PPAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P7F:(2~{R})-2-[3-[[1,3-benzoxazol-2-yl-[3-(4-methoxyphenoxy)propyl]amino]methyl]phenoxy]butanoic+acid'>P7F</scene></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=6l96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l96 OCA], [~~http~~://pdbe.org/6l96 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6l96 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6l96 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6l96 ProSAT]</span></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=6l96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l96 OCA], [https://pdbe.org/6l96 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l96 RCSB], [https://www.ebi.ac.uk/pdbsum/6l96 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l96 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PPARA_HUMAN PPARA_HUMAN]] Ligand-activated transcription factor. Key regulator of lipid metabolism. Activated by the endogenous ligand 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (16:0/18:1-GPC). Activated by oleylethanolamide, a naturally occurring lipid that regulates satiety (By similarity). Receptor for peroxisome proliferators such as hypolipidemic drugs and fatty acids. Regulates the peroxisomal beta-oxidation pathway of fatty acids. Functions as transcription activator for the ACOX1 and P450 genes. Transactivation activity requires heterodimerization with RXRA and is antagonized by NR2C2.<ref>PMID:7684926</ref> <ref>PMID:7629123</ref> <ref>PMID:9556573</ref> <ref>PMID:10195690</ref>	+	[https://www.uniprot.org/uniprot/PPARA_HUMAN PPARA_HUMAN] Ligand-activated transcription factor. Key regulator of lipid metabolism. Activated by the endogenous ligand 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (16:0/18:1-GPC). Activated by oleylethanolamide, a naturally occurring lipid that regulates satiety (By similarity). Receptor for peroxisome proliferators such as hypolipidemic drugs and fatty acids. Regulates the peroxisomal beta-oxidation pathway of fatty acids. Functions as transcription activator for the ACOX1 and P450 genes. Transactivation activity requires heterodimerization with RXRA and is antagonized by NR2C2.<ref>PMID:7684926</ref> <ref>PMID:7629123</ref> <ref>PMID:9556573</ref> <ref>PMID:10195690</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6l96" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6l96" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Peroxisome proliferator-activated receptor 3D structures\|Peroxisome proliferator-activated receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arulmozhira, S]]	+	[[Category: Arulmozhira S]]
-	[[Category: Ito, S]]	+	[[Category: Ito S]]
-	[[Category: Kambe, A]]	+	[[Category: Kambe A]]
-	[[Category: Kawasaki, M]]	+	[[Category: Kawasaki M]]
-	[[Category: Nakagawa, Y]]	+	[[Category: Nakagawa Y]]
-	[[Category: Nakano, S]]	+	[[Category: Nakano S]]
-	[[Category: Shimano, H]]	+	[[Category: Shimano H]]
-	[[Category: Tokiwa, H]]	+	[[Category: Tokiwa H]]
-	[[Category: Yamamoto, Y]]	+	[[Category: Yamamoto Y]]
-	~~[[Category: Transcription~~]]	+

OCA at 16:12, 29 January 2020

OCA — Wed, 29 Jan 2020 16:12:24 GMT

←Older revision		Revision as of 16:12, 29 January 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6l96 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structure of PPARalpha-LBD/pemafibrate/SRC1 peptide==
		+	<StructureSection load='6l96' size='340' side='right'caption='[[6l96]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6l96]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6L96 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=P7F:(2~{R})-2-[3-[[1,3-benzoxazol-2-yl-[3-(4-methoxyphenoxy)propyl]amino]methyl]phenoxy]butanoic+acid'>P7F</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPARA, NR1C1, PPAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6l96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l96 OCA], [http://pdbe.org/6l96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l96 RCSB], [http://www.ebi.ac.uk/pdbsum/6l96 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l96 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PPARA_HUMAN PPARA_HUMAN]] Ligand-activated transcription factor. Key regulator of lipid metabolism. Activated by the endogenous ligand 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (16:0/18:1-GPC). Activated by oleylethanolamide, a naturally occurring lipid that regulates satiety (By similarity). Receptor for peroxisome proliferators such as hypolipidemic drugs and fatty acids. Regulates the peroxisomal beta-oxidation pathway of fatty acids. Functions as transcription activator for the ACOX1 and P450 genes. Transactivation activity requires heterodimerization with RXRA and is antagonized by NR2C2.<ref>PMID:7684926</ref> <ref>PMID:7629123</ref> <ref>PMID:9556573</ref> <ref>PMID:10195690</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The selective PPARalpha modulator (SPPARMalpha) is expected to medicate dyslipidemia with minimizing adverse effects. Recently, pemafibrate was screened from the ligand library as an SPPARMalpha bearing strong potency. Several clinical pieces of evidence have proved the usefulness of pemafibrate as a medication; however, how pemafibrate works as a SPPARMalpha at the molecular level is not fully known. In this study, we investigate the molecular mechanism behind its novel SPPARMalpha character through a combination of approaches of X-ray crystallography, isothermal titration calorimetry (ITC), and fragment molecular orbital (FMO) analysis. ITC measurements have indicated that pemafibrate binds more strongly to PPARalpha than to PPARgamma. The crystal structure of PPARalpha-ligand binding domain (LBD)/pemafibrate/steroid receptor coactivator-1 peptide (SRC1) determined at 3.2 A resolution indicates that pemafibrate binds to the ligand binding pocket (LBP) of PPARalpha in a Y-shaped form. The structure also reveals that the conformation of the phenoxyalkyl group in pemafibrate is flexible in the absence of SRC1 coactivator peptide bound to PPARalpha; this gives a freedom for the phenoxyalkyl group to adopt structural changes induced by the binding of coactivators. FMO calculations have indicated that the accumulation of hydrophobic interactions provided by the residues at the LBP improve the interaction between pemafibrate and PPARalpha compared with the interaction between fenofibrate and PPARalpha.

-	~~Authors~~:	+	Elucidation of Molecular Mechanism of a Selective PPARalpha Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography, Thermodynamic Analysis, and First-Principle Calculations.,Kawasaki M, Kambe A, Yamamoto Y, Arulmozhiraja S, Ito S, Nakagawa Y, Tokiwa H, Nakano S, Shimano H Int J Mol Sci. 2020 Jan 6;21(1). pii: ijms21010361. doi: 10.3390/ijms21010361. PMID:31935812<ref>PMID:31935812</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6l96" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
		+	[[Category: Arulmozhira, S]]
		+	[[Category: Ito, S]]
		+	[[Category: Kambe, A]]
		+	[[Category: Kawasaki, M]]
		+	[[Category: Nakagawa, Y]]
		+	[[Category: Nakano, S]]
		+	[[Category: Shimano, H]]
		+	[[Category: Tokiwa, H]]
		+	[[Category: Yamamoto, Y]]
		+	[[Category: Transcription]]

OCA at 06:31, 1 January 2020

OCA — Wed, 01 Jan 2020 06:31:16 GMT

←Older revision		Revision as of 06:31, 1 January 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6l96 is ON HOLD	+	The entry 6l96 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6l96" [edit=sysop:move=sysop]

OCA — Wed, 13 Nov 2019 09:19:21 GMT

Protected "6l96" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:19, 13 November 2019

OCA: New page: '''Unreleased structure''' The entry 6l96 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Nov 2019 09:19:19 GMT

New page: '''Unreleased structure''' The entry 6l96 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6l96 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]