1yv5 - Revision history

OCA at 08:12, 25 October 2023

OCA — Wed, 25 Oct 2023 08:12:54 GMT

←Older revision		Revision as of 08:12, 25 October 2023
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	<StructureSection load='1yv5' size='340' side='right'caption='[[1yv5]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1yv5' size='340' side='right'caption='[[1yv5]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yv5]] is a 1 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=1YV5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1YV5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yv5]] is a 1 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=1YV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YV5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIS:1-HYDROXY-~~2~~-(3-PYRIDINYL)ETHYLIDENE+BIS-PHOSPHONIC+ACID'>RIS</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1yq7\|1yq7]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIS:1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE+BIS-PHOSPHONIC+ACID'>RIS</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene:]]</b></td><td class~~=~~"sblockDat">FDPS ([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'>[https://proteopedia.org/fgij/fg.htm?mol=1yv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv5 OCA], [https://pdbe.org/1yv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yv5 RCSB], [https://www.ebi.ac.uk/pdbsum/1yv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yv5 ProSAT]</span></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/~~(~~2E,6E)~~-~~farnesyl_diphosphate_synthase (2E,6E~~)-~~farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10]~~ </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1yv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv5 OCA], [~~http~~://pdbe.org/1yv5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yv5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yv5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yv5 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FPPS_HUMAN FPPS_HUMAN]] Key enzyme in isoprenoid biosynthesis which catalyzes the formation of farnesyl diphosphate (FPP), a precursor for several classes of essential metabolites including sterols, dolichols, carotenoids, and ubiquinones. FPP also serves as substrate for protein farnesylation and geranylgeranylation. Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.	+	[https://www.uniprot.org/uniprot/FPPS_HUMAN FPPS_HUMAN] Key enzyme in isoprenoid biosynthesis which catalyzes the formation of farnesyl diphosphate (FPP), a precursor for several classes of essential metabolites including sterols, dolichols, carotenoids, and ubiquinones. FPP also serves as substrate for protein farnesylation and geranylgeranylation. Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arrowsmith, C]]	+	[[Category: Arrowsmith C]]
-	~~[[Category: Delft, F Von~~]]	+	[[Category: Edwards A]]
-	[[Category: Edwards, A]]	+	[[Category: Guo K]]
-	[[Category: Guo, K]]	+	[[Category: Kavanagh KL]]
-	[[Category: Kavanagh~~, K L~~]]	+	[[Category: Oppermann U]]
-	[[Category: Oppermann, U]]	+	[[Category: Sundstrom M]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Von Delft F]]
-	[[Category: Sundstrom, M]]	+
-	[[Category: ~~Bisphosphonate]]~~	+
-	~~[[Category: Cholesterol synthesis]]~~	+
-	~~[[Category: Isoprenoid pathway]]~~	+
-	~~[[Category: Sgc]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:53, 20 January 2021

OCA — Wed, 20 Jan 2021 08:53:20 GMT

←Older revision		Revision as of 08:53, 20 January 2021
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	==Human farnesyl diphosphate synthase complexed with Mg and risedronate==		==Human farnesyl diphosphate synthase complexed with Mg and risedronate==
-	<StructureSection load='1yv5' size='340' side='right' caption='[[1yv5]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1yv5' size='340' side='right'caption='[[1yv5]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yv5]] is a 1 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=1YV5 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YV5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yv5]] is a 1 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=1YV5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YV5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIS:1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE+BIS-PHOSPHONIC+ACID'>RIS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIS:1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE+BIS-PHOSPHONIC+ACID'>RIS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yq7\|1yq7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yq7\|1yq7]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FDPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FDPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></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=1yv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv5 OCA], [http://pdbe.org/1yv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1yv5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yv5 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1yv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv5 OCA], [http://pdbe.org/1yv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1yv5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yv5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[Farnesyl diphosphate synthase\|Farnesyl diphosphate synthase]]	+	*[[Farnesyl diphosphate synthase 3D structures\|Farnesyl diphosphate synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arrowsmith, C]]		[[Category: Arrowsmith, C]]
	[[Category: Delft, F Von]]		[[Category: Delft, F Von]]

OCA at 06:35, 25 April 2018

OCA — Wed, 25 Apr 2018 06:35:02 GMT

←Older revision		Revision as of 06:35, 25 April 2018
Line 1:		Line 1:
		+
	==Human farnesyl diphosphate synthase complexed with Mg and risedronate==		==Human farnesyl diphosphate synthase complexed with Mg and risedronate==
	<StructureSection load='1yv5' size='340' side='right' caption='[[1yv5]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1yv5' size='340' side='right' caption='[[1yv5]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FDPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FDPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></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=1yv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv5 OCA], [http://pdbe.org/1yv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1yv5 PDBsum]</span></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=1yv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv5 OCA], [http://pdbe.org/1yv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1yv5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yv5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yv/1yv5_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yv/1yv5_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 02:19, 7 February 2016

OCA — Sun, 07 Feb 2016 02:19:26 GMT

←Older revision		Revision as of 02:19, 7 February 2016
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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].	+	</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=1yv5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:44, 9 September 2015

OCA — Wed, 09 Sep 2015 20:44:33 GMT

←Older revision		Revision as of 20:44, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1yv5' size='340' side='right' caption='[[1yv5]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1yv5' size='340' side='right' caption='[[1yv5]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YV5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yv5]] is a 1 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=1YV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YV5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIS:1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE+BIS-PHOSPHONIC+ACID'>RIS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIS:1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE+BIS-PHOSPHONIC+ACID'>RIS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yq7\|1yq7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yq7\|1yq7]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FDPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FDPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Geranyltranstransferase Geranyltranstransferase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></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=1yv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1yv5 PDBsum]</span></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=1yv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv5 OCA], [http://pdbe.org/1yv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1yv5 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 1yv5" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geranyltranstransferase]]~~	+	[[Category: Human]]
-	~~[[Category: Homo sapiens~~]]	+
	[[Category: Arrowsmith, C]]		[[Category: Arrowsmith, C]]
	[[Category: Delft, F Von]]		[[Category: Delft, F Von]]

OCA at 07:02, 24 December 2014

OCA — Wed, 24 Dec 2014 07:02:08 GMT

←Older revision		Revision as of 07:02, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YV5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YV5 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIS:1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE+BIS-PHOSPHONIC+ACID'>RIS</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIS:1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE+BIS-PHOSPHONIC+ACID'>RIS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yq7\|1yq7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yq7\|1yq7]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FDPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FDPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Geranyltranstransferase Geranyltranstransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Geranyltranstransferase Geranyltranstransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></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=1yv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1yv5 PDBsum]</span></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=1yv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1yv5 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FPPS_HUMAN FPPS_HUMAN]] Key enzyme in isoprenoid biosynthesis which catalyzes the formation of farnesyl diphosphate (FPP), a precursor for several classes of essential metabolites including sterols, dolichols, carotenoids, and ubiquinones. FPP also serves as substrate for protein farnesylation and geranylgeranylation. Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Geranyltranstransferase]]		[[Category: Geranyltranstransferase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Arrowsmith, C.]]	+	[[Category: Arrowsmith, C]]
-	[[Category: Delft, F Von.]]	+	[[Category: Delft, F Von]]
-	[[Category: Edwards, A.]]	+	[[Category: Edwards, A]]
-	[[Category: Guo, K.]]	+	[[Category: Guo, K]]
-	[[Category: Kavanagh, K L.]]	+	[[Category: Kavanagh, K L]]
-	[[Category: Oppermann, U.]]	+	[[Category: Oppermann, U]]
-	[[Category: ~~SGC,~~ Structural ~~Genomics Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sundstrom, M.]]	+	[[Category: Sundstrom, M]]
	[[Category: Bisphosphonate]]		[[Category: Bisphosphonate]]
	[[Category: Cholesterol synthesis]]		[[Category: Cholesterol synthesis]]
	[[Category: Isoprenoid pathway]]		[[Category: Isoprenoid pathway]]
	[[Category: Sgc]]		[[Category: Sgc]]
-	[[Category: Structural genomic]]
-	[[Category: Structural genomics consortium]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 19:27, 28 September 2014

OCA — Sun, 28 Sep 2014 19:27:52 GMT

←Older revision		Revision as of 19:27, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1yv5.~~png~~\|~~left~~\|200px]]	+	==Human farnesyl diphosphate synthase complexed with Mg and risedronate==
		+	<StructureSection load='1yv5' size='340' side='right' caption='[[1yv5]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YV5 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RIS:1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE+BIS-PHOSPHONIC+ACID'>RIS</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yq7\|1yq7]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FDPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Geranyltranstransferase Geranyltranstransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></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=1yv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yv5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1yv5 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/yv/1yv5_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 ==
		+	Osteoporosis and low bone mass are currently estimated to be a major public health risk affecting >50% of the female population over the age of 50. Because of their bone-selective pharmacokinetics, nitrogen-containing bisphosphonates (N-BPs), currently used as clinical inhibitors of bone-resorption diseases, target osteoclast farnesyl pyrophosphate synthase (FPPS) and inhibit protein prenylation. FPPS, a key branchpoint of the mevalonate pathway, catalyzes the successive condensation of isopentenyl pyrophosphate with dimethylallyl pyrophosphate and geranyl pyrophosphate. To understand the molecular events involved in inhibition of FPPS by N-BPs, we used protein crystallography, enzyme kinetics, and isothermal titration calorimetry. We report here high-resolution x-ray structures of the human enzyme in complexes with risedronate and zoledronate, two of the leading N-BPs in clinical use. These agents bind to the dimethylallyl/geranyl pyrophosphate ligand pocket and induce a conformational change. The interactions of the N-BP cyclic nitrogen with Thr-201 and Lys-200 suggest that these inhibitors achieve potency by positioning their nitrogen in the proposed carbocation-binding site. Kinetic analyses reveal that inhibition is competitive with geranyl pyrophosphate and is of a slow, tight binding character, indicating that isomerization of an initial enzyme-inhibitor complex occurs with inhibitor binding. Isothermal titration calorimetry indicates that binding of N-BPs to the apoenzyme is entropy-driven, presumably through desolvation entropy effects. These experiments reveal the molecular binding characteristics of an important pharmacological target and provide a route for further optimization of these important drugs.

-	~~{{STRUCTURE_1yv5\| PDB=1yv5 \| SCENE= }}~~	+	The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs.,Kavanagh KL, Guo K, Dunford JE, Wu X, Knapp S, Ebetino FH, Rogers MJ, Russell RG, Oppermann U Proc Natl Acad Sci U S A. 2006 May 16;103(20):7829-34. Epub 2006 May 9. PMID:16684881<ref>PMID:16684881</ref>

-	~~===Human farnesyl diphosphate synthase complexed with Mg and risedronate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16684881}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1yv5]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1YV5 OCA].~~	+

	==See Also==		==See Also==
	*[[Farnesyl diphosphate synthase\|Farnesyl diphosphate synthase]]		*[[Farnesyl diphosphate synthase\|Farnesyl diphosphate synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016684881<~~/~~ref~~><~~ref group="xtra">PMID:019245203</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Geranyltranstransferase]]		[[Category: Geranyltranstransferase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 05:19, 20 October 2012

OCA — Sat, 20 Oct 2012 05:19:33 GMT

←Older revision		Revision as of 05:19, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1yv5]] is a 1 chain structure ~~of [[Farnesyl diphosphate synthase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YV5 OCA].	+	[[1yv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YV5 OCA].

	==See Also==		==See Also==

OCA: Protected "1yv5" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 09:40:49 GMT

Protected "1yv5" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:40, 25 July 2012

OCA at 09:40, 25 July 2012

OCA — Wed, 25 Jul 2012 09:40:48 GMT

←Older revision		Revision as of 09:40, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1yv5.png\|left\|200px]]		[[Image:1yv5.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1yv5", 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_1yv5\| PDB=1yv5 \| SCENE= }}		{{STRUCTURE_1yv5\| PDB=1yv5 \| SCENE= }}

	===Human farnesyl diphosphate synthase complexed with Mg and risedronate===		===Human farnesyl diphosphate synthase complexed with Mg and risedronate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16684881}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16684881 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16684881}}		{{ABSTRACT_PUBMED_16684881}}

	==About this Structure==		==About this Structure==
-	~~1YV5~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YV5 OCA].	+	[[1yv5]] is a 1 chain structure of [[Farnesyl diphosphate synthase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YV5 OCA].
		+
		+	==See Also==
		+	*[[Farnesyl diphosphate synthase\|Farnesyl diphosphate synthase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16684881~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016684881</ref><ref group="xtra">PMID:019245203</ref><references group="xtra"/>
	[[Category: Geranyltranstransferase]]		[[Category: Geranyltranstransferase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
Line 41:		Line 32:
	[[Category: Structural genomics consortium]]		[[Category: Structural genomics consortium]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 13 13:06:02 2010''