3zl6 - Revision history

OCA at 11:05, 20 December 2023

2023-12-20T11:05:02Z

←Older revision		Revision as of 11:05, 20 December 2023
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	<StructureSection load='3zl6' size='340' side='right'caption='[[3zl6]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3zl6' size='340' side='right'caption='[[3zl6]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zl6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZL6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZL6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zl6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZL6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZL6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NVU:2-(1,2-BENZOXAZOL-3-YL)ETHANOIC+ACID'>NVU</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]] 1.85Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NVU:2-(1,2-BENZOXAZOL-3-YL)ETHANOIC+ACID'>NVU</scene></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=3zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zl6 OCA], [https://pdbe.org/3zl6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zl6 RCSB], [https://www.ebi.ac.uk/pdbsum/3zl6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zl6 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=3zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zl6 OCA], [https://pdbe.org/3zl6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zl6 RCSB], [https://www.ebi.ac.uk/pdbsum/3zl6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zl6 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9HWY4_PSEAE Q9HWY4_PSEAE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Schmidberger~~, J W~~]]	+	[[Category: Schmidberger JW]]
-	[[Category: Schneider, G]]	+	[[Category: Schneider G]]
-	[[Category: Schnell, R]]	+	[[Category: Schnell R]]
-	~~[[Category: Km10833]]~~	+
-	~~[[Category: Maybridge fragment library]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 05:50, 10 August 2022

2022-08-10T05:50:21Z

←Older revision		Revision as of 05:50, 10 August 2022
Line 1:		Line 1:

	==Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833.==		==Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833.==
-	<StructureSection load='3zl6' size='340' side='right' caption='[[3zl6]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='3zl6' size='340' side='right'caption='[[3zl6]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zl6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZL6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ZL6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zl6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZL6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZL6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NVU:2-(1,2-BENZOXAZOL-3-YL)ETHANOIC+ACID'>NVU</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NVU:2-(1,2-BENZOXAZOL-3-YL)ETHANOIC+ACID'>NVU</scene></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'>[https://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [https://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=3zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zl6 OCA], [~~http~~://pdbe.org/3zl6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3zl6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3zl6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3zl6 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=3zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zl6 OCA], [https://pdbe.org/3zl6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zl6 RCSB], [https://www.ebi.ac.uk/pdbsum/3zl6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zl6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pseae]]		[[Category: Pseae]]
	[[Category: Schmidberger, J W]]		[[Category: Schmidberger, J W]]

OCA at 16:50, 2 January 2017

2017-01-02T16:50:41Z

←Older revision		Revision as of 16:50, 2 January 2017
Line 1:		Line 1:
		+
	==Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833.==		==Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833.==
	<StructureSection load='3zl6' size='340' side='right' caption='[[3zl6]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3zl6' size='340' side='right' caption='[[3zl6]], [[Resolution\|resolution]] 1.85Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NVU:2-(1,2-BENZOXAZOL-3-YL)ETHANOIC+ACID'>NVU</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NVU:2-(1,2-BENZOXAZOL-3-YL)ETHANOIC+ACID'>NVU</scene></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=3zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zl6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zl6 RCSB], [http://www.ebi.ac.uk/pdbsum/3zl6 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=3zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zl6 OCA], [http://pdbe.org/3zl6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zl6 RCSB], [http://www.ebi.ac.uk/pdbsum/3zl6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zl6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 3zl6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:18, 26 March 2015

2015-03-26T07:18:48Z

←Older revision		Revision as of 07:18, 26 March 2015
Line 7:		Line 7:
	<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=3zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zl6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zl6 RCSB], [http://www.ebi.ac.uk/pdbsum/3zl6 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=3zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zl6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zl6 RCSB], [http://www.ebi.ac.uk/pdbsum/3zl6 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Locus PA4043 in the genome of Pseudomonas aeruginosa PAO1 has been annotated as coding for a farnesyl pyrophosphate synthase (FPPS). This open reading frame was cloned and expressed recombinantly in Escherichia coli. The dimeric enzyme shows farnesyl pyrophosphate synthase activity and is strongly inhibited by ibandronate and zoledronate, drugs that are presently in clinical use. The structures of the unliganded enzyme and complexes with the substrate geranyl diphosphate (GPP), the inhibitor ibandronate and two compounds obtained from a differential scanning fluorimetry-based screen of a fragment library were determined by X-ray crystallography to resolutions of better than 2.0 A. The enzyme shows the typical alpha-helical fold of farnesyl pyrophosphate synthases. The substrate GPP binds in the S1 substrate site in an open conformation of the enzyme. In the enzyme-ibandronate complex three inhibitor molecules are bound in the active site of the enzyme. One inhibitor molecule occupies the allylic substrate site (S1) of each subunit, as observed in complexes of nitrogen-containing bisphosphonate inhibitors of farnesyl synthases from other species. Two (in subunit A) and one (in subunit B) additional ibandronate molecules are bound in the active site. The structures of the fragment complexes show two molecules bound in a hydrophobic pocket adjacent to the active site. This allosteric pocket, which has previously only been described for FPPS from eukaryotic organisms, is thus also present in enzymes from pathogenic prokaryotes and might be utilized for the design of inhibitors of bacterial FPPS with a different chemical scaffold to the highly charged bisphosphonates, which are less likely to pass bacterial membranes.
		+
		+	Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase from Pseudomonas aeruginosa.,Schmidberger JW, Schnell R, Schneider G Acta Crystallogr D Biol Crystallogr. 2015 Mar 1;71(Pt 3):721-31. doi:, 10.1107/S1399004715001121. Epub 2015 Feb 26. PMID:25760619<ref>PMID:25760619</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:04, 21 December 2014

2014-12-21T17:04:23Z

←Older revision		Revision as of 17:04, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3zl6\| PDB=3zl6 \| SCENE= }}~~	+	==Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833.==
-	===Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833.===	+	<StructureSection load='3zl6' size='340' side='right' caption='[[3zl6]], [[Resolution\|resolution]] 1.85Å' scene=''>
-		+	== Structural highlights ==
-	==~~About this Structure~~==	+	<table><tr><td colspan='2'>[[3zl6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZL6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZL6 FirstGlance]. <br>
-	[[3zl6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZL6 OCA].	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NVU:2-(1,2-BENZOXAZOL-3-YL)ETHANOIC+ACID'>NVU</scene></td></tr>
-	[[Category: Schmidberger, J W.]]	+	<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>
-	[[Category: Schneider, G.]]	+	<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=3zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zl6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zl6 RCSB], [http://www.ebi.ac.uk/pdbsum/3zl6 PDBsum]</span></td></tr>
-	[[Category: Schnell, R.]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Pseae]]
		+	[[Category: Schmidberger, J W]]
		+	[[Category: Schneider, G]]
		+	[[Category: Schnell, R]]
	[[Category: Km10833]]		[[Category: Km10833]]
	[[Category: Maybridge fragment library]]		[[Category: Maybridge fragment library]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 05:13, 13 February 2014

2014-02-13T05:13:38Z

←Older revision		Revision as of 05:13, 13 February 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3zl6\| PDB=3zl6 \| SCENE= }}
		+	===Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833.===

-	~~The entry~~ 3zl6 is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[3zl6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZL6 OCA].
-	~~Authors~~: Schmidberger, J.W., Schnell, R.~~, Schneider, G.~~	+	[[Category: Schmidberger, J W.]]
-		+	[[Category: Schneider, G.]]
-	~~Description~~: ~~Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound~~ fragment ~~KM10833.~~	+	[[Category: Schnell, R.]]
		+	[[Category: Km10833]]
		+	[[Category: Maybridge fragment library]]
		+	[[Category: Transferase]]

OCA: Protected "3zl6" [edit=sysop:move=sysop]

2013-02-06T12:16:00Z

Protected "3zl6" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:16, 6 February 2013

OCA: New page: '''Unreleased structure''' The entry 3zl6 is ON HOLD until Paper Publication Authors: Schmidberger, J.W., Schnell, R., Schneider, G. Description: Native structure of Farnesyl Pyrophosp...

2013-02-06T12:15:59Z

New page: '''Unreleased structure''' The entry 3zl6 is ON HOLD until Paper Publication Authors: Schmidberger, J.W., Schnell, R., Schneider, G. Description: Native structure of Farnesyl Pyrophosp...

New page

'''Unreleased structure'''

The entry 3zl6 is ON HOLD until Paper Publication

Authors: Schmidberger, J.W., Schnell, R., Schneider, G.

Description: Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound fragment KM10833.