3g6n - Revision history

OCA at 15:37, 1 November 2023

OCA — Wed, 01 Nov 2023 15:37:00 GMT

←Older revision		Revision as of 15:37, 1 November 2023
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	<StructureSection load='3g6n' size='340' side='right'caption='[[3g6n]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3g6n' size='340' side='right'caption='[[3g6n]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g6n]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_19434 Atcc 19434~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3G6N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g6n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G6N FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[3cmd\|3cmd]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [https://pdbe.org/3g6n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [https://www.ebi.ac.uk/pdbsum/3g6n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g6n 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=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [~~http~~://pdbe.org/3g6n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3g6n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3g6n ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q842S4_ENTFC Q842S4_ENTFC]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).[HAMAP-Rule:MF_00163]	+	[https://www.uniprot.org/uniprot/Q842S4_ENTFC Q842S4_ENTFC] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).[HAMAP-Rule:MF_00163]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 19434~~]]	+	[[Category: Enterococcus faecium]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Peptide deformylase]]~~	+	[[Category: Hwang KY]]
-	[[Category: Hwang~~, K Y~~]]	+	[[Category: Nam KH]]
-	[[Category: Nam~~, K H]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pdf~~]]	+

OCA at 10:37, 9 September 2020

OCA — Wed, 09 Sep 2020 10:37:13 GMT

←Older revision		Revision as of 10:37, 9 September 2020
Line 1:		Line 1:

	==Crystal structure of an EfPDF complex with Met-Ala-Ser==		==Crystal structure of an EfPDF complex with Met-Ala-Ser==
-	<StructureSection load='3g6n' size='340' side='right' caption='[[3g6n]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='3g6n' size='340' side='right'caption='[[3g6n]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g6n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3G6N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g6n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3G6N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cmd\|3cmd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cmd\|3cmd]]</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=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [http://pdbe.org/3g6n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [http://www.ebi.ac.uk/pdbsum/3g6n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g6n 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=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [http://pdbe.org/3g6n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [http://www.ebi.ac.uk/pdbsum/3g6n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g6n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 19434]]		[[Category: Atcc 19434]]
		+	[[Category: Large Structures]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Hwang, K Y]]		[[Category: Hwang, K Y]]

OCA at 08:03, 5 December 2018

OCA — Wed, 05 Dec 2018 08:03:59 GMT

←Older revision		Revision as of 08:03, 5 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of an EfPDF complex with Met-Ala-Ser==		==Crystal structure of an EfPDF complex with Met-Ala-Ser==
	<StructureSection load='3g6n' size='340' side='right' caption='[[3g6n]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3g6n' size='340' side='right' caption='[[3g6n]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cmd\|3cmd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cmd\|3cmd]]</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=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [http://pdbe.org/3g6n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [http://www.ebi.ac.uk/pdbsum/3g6n 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=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [http://pdbe.org/3g6n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [http://www.ebi.ac.uk/pdbsum/3g6n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g6n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g6/3g6n_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g6/3g6n_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 15:40, 8 February 2016

OCA — Mon, 08 Feb 2016 15:40:07 GMT

←Older revision		Revision as of 15:40, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3g6n' size='340' side='right' caption='[[3g6n]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3g6n' size='340' side='right' caption='[[3g6n]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g6n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterococcus_faecium Enterococcus faecium~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G6N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g6n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G6N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cmd\|3cmd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cmd\|3cmd]]</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=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [http://www.ebi.ac.uk/pdbsum/3g6n 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=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [http://pdbe.org/3g6n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [http://www.ebi.ac.uk/pdbsum/3g6n PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=3g6n ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 3g6n" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterococcus faecium~~]]	+	[[Category: Atcc 19434]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Hwang, K Y]]		[[Category: Hwang, K Y]]

OCA at 00:24, 25 December 2014

OCA — Thu, 25 Dec 2014 00:24:04 GMT

←Older revision		Revision as of 00:24, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3g6n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G6N FirstGlance]. <br>		<table><tr><td colspan='2'>[[3g6n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G6N FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cmd\|3cmd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cmd\|3cmd]]</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=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [http://www.ebi.ac.uk/pdbsum/3g6n 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=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [http://www.ebi.ac.uk/pdbsum/3g6n PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q842S4_ENTFC Q842S4_ENTFC]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).[HAMAP-Rule:MF_00163]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 24:		Line 26:
	Crystal structure of an EfPDF complex with Met-Ala-Ser based on crystallographic packing.,Nam KH, Kim KH, Kim EE, Hwang KY Biochem Biophys Res Commun. 2009 Apr 17;381(4):630-3. Epub 2009 Feb 26. PMID:19249287<ref>PMID:19249287</ref>		Crystal structure of an EfPDF complex with Met-Ala-Ser based on crystallographic packing.,Nam KH, Kim KH, Kim EE, Hwang KY Biochem Biophys Res Commun. 2009 Apr 17;381(4):630-3. Epub 2009 Feb 26. PMID:19249287<ref>PMID:19249287</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 32:		Line 34:
	[[Category: Enterococcus faecium]]		[[Category: Enterococcus faecium]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
-	[[Category: Hwang, K Y.]]	+	[[Category: Hwang, K Y]]
-	[[Category: Nam, K H.]]	+	[[Category: Nam, K H]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Pdf]]		[[Category: Pdf]]
-	[[Category: Peptide deformylase]]

OCA at 09:49, 21 May 2014

OCA — Wed, 21 May 2014 09:49:59 GMT

←Older revision		Revision as of 09:49, 21 May 2014
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-	[[~~Image:~~3g6n.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of an EfPDF complex with Met-Ala-Ser==
		+	<StructureSection load='3g6n' size='340' side='right' caption='[[3g6n]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3g6n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G6N FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cmd\|3cmd]]</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=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [http://www.ebi.ac.uk/pdbsum/3g6n 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/g6/3g6n_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 ==
		+	PDF (peptide deformylase) plays a critical role in the production of mature proteins by removing the N-formyl polypeptide of nascent proteins in the prokaryote cell system. This protein is essential for bacterial growth, making it an attractive target for the design of new antibiotics. Accordingly, PDF has been evaluated as a drug target; however, architectural mechanism studies of PDF have not yet fully elucidated its molecular function. We recently reported the crystal structure of PDF produced by Enterococcus faecium [K.H. Nam, J.I. Ham, A. Priyadarshi, E.E. Kim, N. Chung, K.Y. Hwang, "Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure", Proteins 74 (2009) 261-265]. Here, we present the crystal structure of the EfPDF complex with MAS (Met-Ser-Ala), thereby not only delineating the architectural mechanism for the recognition of mimic-peptides by N-terminal cleaved expression peptide, but also suggesting possible targets for rational design of antibacterial drugs. In addition to their implications for drug design, these structural studies will facilitate elucidation of the architectural mechanism responsible for the peptide recognition of PDF.

-	<!--	+	Crystal structure of an EfPDF complex with Met-Ala-Ser based on crystallographic packing.,Nam KH, Kim KH, Kim EE, Hwang KY Biochem Biophys Res Commun. 2009 Apr 17;381(4):630-3. Epub 2009 Feb 26. PMID:19249287<ref>PMID:19249287</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3g6n"~~, ~~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_3g6n\| PDB=3g6n \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~an EfPDF complex with Met-Ala-Ser===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_19249287}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 19249287 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_19249287}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3g6n]] is a 4 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019249287<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Enterococcus faecium]]		[[Category: Enterococcus faecium]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]

OCA: Protected "3g6n" [edit=sysop:move=sysop]

OCA — Wed, 22 Feb 2012 07:02:11 GMT

Protected "3g6n" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:02, 22 February 2012

OCA at 07:02, 22 February 2012

OCA — Wed, 22 Feb 2012 07:02:09 GMT

←Older revision		Revision as of 07:02, 22 February 2012
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-	{{Seed}}
	[[Image:3g6n.png\|left\|200px]]		[[Image:3g6n.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~3G6N~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA].	+	[[3g6n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19249287~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019249287</ref><references group="xtra"/>
	[[Category: Enterococcus faecium]]		[[Category: Enterococcus faecium]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
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	[[Category: Pdf]]		[[Category: Pdf]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 29 20:43:47 2009''

OCA at 17:43, 29 April 2009

OCA — Wed, 29 Apr 2009 17:43:48 GMT

←Older revision		Revision as of 17:43, 29 April 2009
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	{{Seed}}		{{Seed}}
-	[[Image:3g6n.~~jpg~~\|left\|200px]]	+	[[Image:3g6n.png\|left\|200px]]

	<!--		<!--
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	===Crystal structure of an EfPDF complex with Met-Ala-Ser===		===Crystal structure of an EfPDF complex with Met-Ala-Ser===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19249287}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19249287 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19249287}}

	==About this Structure==		==About this Structure==
	3G6N is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA].		3G6N is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19249287</ref><references group="xtra"/>
	[[Category: Enterococcus faecium]]		[[Category: Enterococcus faecium]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
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	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 4 15~~:00:40 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 29 20:43:47 2009''

OCA at 13:00, 4 March 2009

OCA — Wed, 04 Mar 2009 13:00:41 GMT

←Older revision		Revision as of 13:00, 4 March 2009
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3g6n.jpg\|left\|200px]]

-	The ~~entry 3g6n~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3g6n", 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_3g6n\| PDB=3g6n \| SCENE= }}

-	~~Authors: Hwang, K.Y., Nam, K.H.~~	+	===Crystal structure of an EfPDF complex with Met-Ala-Ser===

-	Description: Crystal structure of an EfPDF complex with Met-Ala-Ser

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 25 09~~:27:08 2009''	+	==About this Structure==
		+	3G6N is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6N OCA].
		+	[[Category: Enterococcus faecium]]
		+	[[Category: Peptide deformylase]]
		+	[[Category: Hwang, K Y.]]
		+	[[Category: Nam, K H.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pdf]]
		+	[[Category: Peptide deformylase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 4 15:00:40 2009''