1lqy - Revision history

OCA at 07:35, 14 February 2024

OCA — Wed, 14 Feb 2024 07:35:10 GMT

←Older revision		Revision as of 07:35, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1lqy' size='340' side='right'caption='[[1lqy]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1lqy' size='340' side='right'caption='[[1lqy]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lqy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lqy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LQY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>~~, ~~<scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 1.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1lqw\|1lqw]], [[1lru\|1lru]], [[1lry\|1lry]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88]~~ </~~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=1lqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lqy OCA], [https://pdbe.org/1lqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lqy RCSB], [https://www.ebi.ac.uk/pdbsum/1lqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lqy 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=1lqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lqy OCA], [https://pdbe.org/1lqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lqy RCSB], [https://www.ebi.ac.uk/pdbsum/1lqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lqy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DEF2_GEOSE DEF2_GEOSE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1lqy 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=1lqy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Bacterial peptide deformylase (PDF) belongs to a sub-family of metalloproteases that catalyse the removal of the N-terminal formyl group from newly synthesised proteins. PDF is essential in prokaryotes and conserved throughout the eubacteria. It is therefore considered an attractive target for developing new antibacterial agents. Here, we report the crystal structures of four bacterial deformylases, free or bound to the naturally occurring antibiotic actinonin, including two from the major bacterial pathogens Pseudomonas aeruginosa and Staphylococcus aureus. The overall tertiary structure is essentially conserved but shows significant differences, namely at the C terminus, which are directly related to the deformylase type (i.e. I or II) they belong to. The geometry around the catalytic metal ion exhibits a high level of similarity within the different enzymes, as does the binding mode of actinonin to the various deformylases. However, some significant structural differences are found in the vicinity of the active site, highlighting the structural and molecular requirements for the design of a deformylase inhibitor active against a broad spectrum of bacterial strains.
-
-	The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents.,Guilloteau JP, Mathieu M, Giglione C, Blanc V, Dupuy A, Chevrier M, Gil P, Famechon A, Meinnel T, Mikol V J Mol Biol. 2002 Jul 26;320(5):951-62. PMID:12126617<ref>PMID:12126617</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1lqy" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980~~]]	+	[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Peptide deformylase]]~~	+	[[Category: Mathieu M]]
-	[[Category: Mathieu, M]]	+	[[Category: Mikol V]]
-	[[Category: Mikol, V]]	+
-	~~[[Category: Actinonin]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibition]]~~	+
-	~~[[Category: Polypeptide deformylase~~]]	+

OCA at 05:55, 28 April 2021

OCA — Wed, 28 Apr 2021 05:55:37 GMT

←Older revision		Revision as of 05:55, 28 April 2021
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	<StructureSection load='1lqy' size='340' side='right'caption='[[1lqy]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1lqy' size='340' side='right'caption='[[1lqy]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lqy]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lqy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LQY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lqw\|1lqw]], [[1lru\|1lru]], [[1lry\|1lry]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lqw\|1lqw]], [[1lru\|1lru]], [[1lry\|1lry]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1lqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lqy OCA], [~~http~~://pdbe.org/1lqy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1lqy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1lqy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1lqy 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=1lqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lqy OCA], [https://pdbe.org/1lqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lqy RCSB], [https://www.ebi.ac.uk/pdbsum/1lqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lqy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 09:10, 24 July 2019

OCA — Wed, 24 Jul 2019 09:10:27 GMT

←Older revision		Revision as of 09:10, 24 July 2019
Line 1:		Line 1:

	==Crystal Structure of Bacillus stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin==		==Crystal Structure of Bacillus stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin==
-	<StructureSection load='1lqy' size='340' side='right' caption='[[1lqy]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1lqy' size='340' side='right'caption='[[1lqy]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lqy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LQY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lqy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LQY FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lq/1lqy_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lq/1lqy_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>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 12980]]		[[Category: Atcc 12980]]
		+	[[Category: Large Structures]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Mathieu, M]]		[[Category: Mathieu, M]]

OCA at 10:50, 18 October 2017

OCA — Wed, 18 Oct 2017 10:50:17 GMT

←Older revision		Revision as of 10:50, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of Bacillus stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin==		==Crystal Structure of Bacillus stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin==
	<StructureSection load='1lqy' size='340' side='right' caption='[[1lqy]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1lqy' size='340' side='right' caption='[[1lqy]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lqw\|1lqw]], [[1lru\|1lru]], [[1lry\|1lry]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lqw\|1lqw]], [[1lru\|1lru]], [[1lry\|1lry]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1lqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lqy OCA], [http://pdbe.org/1lqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lqy RCSB], [http://www.ebi.ac.uk/pdbsum/1lqy 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=1lqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lqy OCA], [http://pdbe.org/1lqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lqy RCSB], [http://www.ebi.ac.uk/pdbsum/1lqy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lqy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=1lqy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:43, 11 September 2015

OCA — Fri, 11 Sep 2015 16:43:47 GMT

←Older revision		Revision as of 16:43, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1lqy' size='340' side='right' caption='[[1lqy]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1lqy' size='340' side='right' caption='[[1lqy]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lqy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_stearothermophilus Geobacillus stearothermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lqy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LQY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lqw\|1lqw]], [[1lru\|1lru]], [[1lry\|1lry]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lqw\|1lqw]], [[1lru\|1lru]], [[1lry\|1lry]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1lqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lqy RCSB], [http://www.ebi.ac.uk/pdbsum/1lqy 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=1lqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lqy OCA], [http://pdbe.org/1lqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lqy RCSB], [http://www.ebi.ac.uk/pdbsum/1lqy PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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 1lqy" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geobacillus stearothermophilus~~]]	+	[[Category: Atcc 12980]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Mathieu, M]]		[[Category: Mathieu, M]]

OCA at 19:10, 25 December 2014

OCA — Thu, 25 Dec 2014 19:10:28 GMT

←Older revision		Revision as of 19:10, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lqy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LQY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lqy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LQY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lqw\|1lqw]], [[1lru\|1lru]], [[1lry\|1lry]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lqw\|1lqw]], [[1lru\|1lru]], [[1lry\|1lry]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1lqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lqy RCSB], [http://www.ebi.ac.uk/pdbsum/1lqy 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=1lqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lqy RCSB], [http://www.ebi.ac.uk/pdbsum/1lqy PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
-	[[Category: Mathieu, M.]]	+	[[Category: Mathieu, M]]
-	[[Category: Mikol, V.]]	+	[[Category: Mikol, V]]
	[[Category: Actinonin]]		[[Category: Actinonin]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Inhibition]]		[[Category: Inhibition]]
	[[Category: Polypeptide deformylase]]		[[Category: Polypeptide deformylase]]

OCA at 13:13, 28 September 2014

OCA — Sun, 28 Sep 2014 13:13:38 GMT

←Older revision		Revision as of 13:13, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1lqy.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Bacillus stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin==
		+	<StructureSection load='1lqy' size='340' side='right' caption='[[1lqy]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1lqy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LQY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lqw\|1lqw]], [[1lru\|1lru]], [[1lry\|1lry]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1lqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lqy RCSB], [http://www.ebi.ac.uk/pdbsum/1lqy 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/lq/1lqy_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 ==
		+	Bacterial peptide deformylase (PDF) belongs to a sub-family of metalloproteases that catalyse the removal of the N-terminal formyl group from newly synthesised proteins. PDF is essential in prokaryotes and conserved throughout the eubacteria. It is therefore considered an attractive target for developing new antibacterial agents. Here, we report the crystal structures of four bacterial deformylases, free or bound to the naturally occurring antibiotic actinonin, including two from the major bacterial pathogens Pseudomonas aeruginosa and Staphylococcus aureus. The overall tertiary structure is essentially conserved but shows significant differences, namely at the C terminus, which are directly related to the deformylase type (i.e. I or II) they belong to. The geometry around the catalytic metal ion exhibits a high level of similarity within the different enzymes, as does the binding mode of actinonin to the various deformylases. However, some significant structural differences are found in the vicinity of the active site, highlighting the structural and molecular requirements for the design of a deformylase inhibitor active against a broad spectrum of bacterial strains.

-	~~{{STRUCTURE_1lqy\| PDB=1lqy \| SCENE= }}~~	+	The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents.,Guilloteau JP, Mathieu M, Giglione C, Blanc V, Dupuy A, Chevrier M, Gil P, Famechon A, Meinnel T, Mikol V J Mol Biol. 2002 Jul 26;320(5):951-62. PMID:12126617<ref>PMID:12126617</ref>

-	~~===Crystal Structure~~ of ~~Bacillus stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12126617}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1lqy]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012126617<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]

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

OCA — Wed, 05 Dec 2012 19:52:24 GMT

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

←Older revision

Revision as of 19:52, 5 December 2012

OCA at 19:52, 5 December 2012

OCA — Wed, 05 Dec 2012 19:52:22 GMT

←Older revision		Revision as of 19:52, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1lqy.png\|left\|200px]]		[[Image:1lqy.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1lqy", 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_1lqy\| PDB=1lqy \| SCENE= }}		{{STRUCTURE_1lqy\| PDB=1lqy \| SCENE= }}

	===Crystal Structure of Bacillus stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin===		===Crystal Structure of Bacillus stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12126617}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12126617 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12126617}}		{{ABSTRACT_PUBMED_12126617}}

	==About this Structure==		==About this Structure==
-	~~1LQY~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA].	+	[[1lqy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12126617~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012126617</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
Line 29:		Line 17:
	[[Category: Mikol, V.]]		[[Category: Mikol, V.]]
	[[Category: Actinonin]]		[[Category: Actinonin]]
		+	[[Category: Hydrolase]]
	[[Category: Inhibition]]		[[Category: Inhibition]]
	[[Category: Polypeptide deformylase]]		[[Category: Polypeptide deformylase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:04:02 2009''

OCA at 02:04, 18 February 2009

OCA — Wed, 18 Feb 2009 02:04:03 GMT

←Older revision		Revision as of 02:04, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1LQY is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA].	+	1LQY is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LQY OCA].

	==Reference==		==Reference==
-	The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents., Guilloteau JP, Mathieu M, Giglione C, Blanc V, Dupuy A, Chevrier M, Gil P, Famechon A, Meinnel T, Mikol V, J Mol Biol. 2002 Jul 26;320(5):951-62. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12126617 12126617]~~	+	<ref group="xtra">PMID:12126617</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
-	[[Category: Single protein]]
	[[Category: Mathieu, M.]]		[[Category: Mathieu, M.]]
	[[Category: Mikol, V.]]		[[Category: Mikol, V.]]
Line 33:		Line 32:
	[[Category: Polypeptide deformylase]]		[[Category: Polypeptide deformylase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 2 21~~:50:~~17 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:04:02 2009''