3it9 - Revision history

OCA at 07:57, 6 September 2023

OCA — Wed, 06 Sep 2023 07:57:44 GMT

←Older revision		Revision as of 07:57, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3it9' size='340' side='right'caption='[[3it9]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3it9' size='340' side='right'caption='[[3it9]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3it9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IT9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3it9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IT9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GLC:ALPHA~~-~~D-GLUCOSE'>GLC</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3ita\|3ita]], [[3itb\|3itb]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class~~=~~"sblockDat">DACC ([https~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td~~></tr>	+
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </~~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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [https://pdbe.org/3it9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [https://www.ebi.ac.uk/pdbsum/3it9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3it9 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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [https://pdbe.org/3it9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [https://www.ebi.ac.uk/pdbsum/3it9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3it9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DACC_ECOLI DACC_ECOLI]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.	+	[https://www.uniprot.org/uniprot/DACC_ECOLI DACC_ECOLI] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
	== 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: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]~~	+	[[Category: Chen Y]]
-	[[Category: Chen, Y]]	+	[[Category: Hesek D]]
-	[[Category: Hesek, D]]	+	[[Category: Lee M]]
-	[[Category: Lee, M]]	+	[[Category: Mobashery S]]
-	[[Category: Mobashery, S]]	+	[[Category: Shi Q]]
-	[[Category: Shi, Q]]	+	[[Category: Shoichet BK]]
-	[[Category: Shoichet~~, B K~~]]	+	[[Category: Zhang W]]
-	[[Category: Zhang, W]]	+
-	~~[[Category: Carboxypeptidase]]~~	+
-	~~[[Category: Cell inner membrane]]~~	+
-	~~[[Category: Cell membrane]]~~	+
-	~~[[Category: Cell shape]]~~	+
-	~~[[Category: Cell wall biogenesis/degradation]]~~	+
-	~~[[Category: Dd-carboxypeptidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Pbp6]]~~	+
-	~~[[Category: Penicillin-binding protein]]~~	+
-	~~[[Category: Peptidoglycan]]~~	+
-	~~[[Category: Peptidoglycan synthesis]]~~	+
-	~~[[Category: Protease~~]]	+

OCA at 03:41, 21 April 2022

OCA — Thu, 21 Apr 2022 03:41:24 GMT

←Older revision		Revision as of 03:41, 21 April 2022
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	==Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state==		==Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state==
-	<StructureSection load='3it9' size='340' side='right' caption='[[3it9]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3it9' size='340' side='right'caption='[[3it9]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3it9]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IT9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3it9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IT9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=~~SUC~~:~~SUCROSE~~'>~~SUC~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ita\|3ita]], [[3itb\|3itb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ita\|3ita]], [[3itb\|3itb]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACC ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [~~http~~://pdbe.org/3it9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3it9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3it9 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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [https://pdbe.org/3it9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [https://www.ebi.ac.uk/pdbsum/3it9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3it9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DACC_ECOLI DACC_ECOLI]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.	+	[[https://www.uniprot.org/uniprot/DACC_ECOLI DACC_ECOLI]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/it/3it9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/it/3it9_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 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3it9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3it9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]

OCA at 08:13, 1 November 2017

OCA — Wed, 01 Nov 2017 08:13:34 GMT

←Older revision		Revision as of 08:13, 1 November 2017
Line 1:		Line 1:
		+
	==Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state==		==Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state==
	<StructureSection load='3it9' size='340' side='right' caption='[[3it9]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3it9' size='340' side='right' caption='[[3it9]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [http://pdbe.org/3it9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [http://www.ebi.ac.uk/pdbsum/3it9 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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [http://pdbe.org/3it9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [http://www.ebi.ac.uk/pdbsum/3it9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3it9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 3it9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3it9" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Penicillin-binding protein\|Penicillin-binding protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:48, 8 February 2016

OCA — Mon, 08 Feb 2016 21:48:51 GMT

←Older revision		Revision as of 21:48, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3it9' size='340' side='right' caption='[[3it9]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3it9' size='340' side='right' caption='[[3it9]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3it9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IT9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3it9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IT9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ita\|3ita]], [[3itb\|3itb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ita\|3ita]], [[3itb\|3itb]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [http://www.ebi.ac.uk/pdbsum/3it9 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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [http://pdbe.org/3it9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [http://www.ebi.ac.uk/pdbsum/3it9 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=3it9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3it9" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]

OCA at 02:22, 25 December 2014

OCA — Thu, 25 Dec 2014 02:22:19 GMT

←Older revision		Revision as of 02:22, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3it9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IT9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3it9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IT9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ita\|3ita]], [[3itb\|3itb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ita\|3ita]], [[3itb\|3itb]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [http://www.ebi.ac.uk/pdbsum/3it9 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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [http://www.ebi.ac.uk/pdbsum/3it9 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DACC_ECOLI DACC_ECOLI]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: Chen, Y.]]	+	[[Category: Chen, Y]]
-	[[Category: Hesek, D.]]	+	[[Category: Hesek, D]]
-	[[Category: Lee, M.]]	+	[[Category: Lee, M]]
-	[[Category: Mobashery, S.]]	+	[[Category: Mobashery, S]]
-	[[Category: Shi, Q.]]	+	[[Category: Shi, Q]]
-	[[Category: Shoichet, B K.]]	+	[[Category: Shoichet, B K]]
-	[[Category: Zhang, W.]]	+	[[Category: Zhang, W]]
	[[Category: Carboxypeptidase]]		[[Category: Carboxypeptidase]]
	[[Category: Cell inner membrane]]		[[Category: Cell inner membrane]]

OCA at 13:08, 29 September 2014

OCA — Mon, 29 Sep 2014 13:08:00 GMT

←Older revision		Revision as of 13:08, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3it9.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state==
		+	<StructureSection load='3it9' size='340' side='right' caption='[[3it9]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3it9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IT9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ita\|3ita]], [[3itb\|3itb]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [http://www.ebi.ac.uk/pdbsum/3it9 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/it/3it9_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 ==
		+	Penicillin-binding protein 6 (PBP6) is one of the two main DD-carboxypeptidases in Escherichia coli, which are implicated in maturation of bacterial cell wall and formation of cell shape. Here, we report the first X-ray crystal structures of PBP6, capturing its apo state (2.1 A), an acyl-enzyme intermediate with the antibiotic ampicillin (1.8 A), and for the first time for a PBP, a preacylation complex (a "Michaelis complex", determined at 1.8 A) with a peptidoglycan substrate fragment containing the full pentapeptide, NAM-(L-Ala-D-isoGlu-L-Lys-D-Ala-D-Ala). These structures illuminate the molecular interactions essential for ligand recognition and catalysis by DD-carboxypeptidases, and suggest a coupling of conformational flexibility of active site loops to the reaction coordinate. The substrate fragment complex structure, in particular, provides templates for models of cell wall recognition by PBPs, as well as substantiating evidence for the molecular mimicry by beta-lactam antibiotics of the peptidoglycan acyl-D-Ala-D-Ala moiety.

-	~~{{STRUCTURE_3it9\| PDB=3it9 \| SCENE= }}~~	+	Crystal structures of penicillin-binding protein 6 from Escherichia coli.,Chen Y, Zhang W, Shi Q, Hesek D, Lee M, Mobashery S, Shoichet BK J Am Chem Soc. 2009 Oct 14;131(40):14345-54. PMID:19807181<ref>PMID:19807181</ref>

-	~~===Crystal structure~~ of ~~Penicillin-Binding Protein 6 (PBP6) from E~~. ~~coli in apo state===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19807181}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3it9]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA].~~	+

	==See Also==		==See Also==
-	*[[Carboxypeptidase\|Carboxypeptidase]]
	*[[Penicillin-binding protein\|Penicillin-binding protein]]		*[[Penicillin-binding protein\|Penicillin-binding protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019807181<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]

OCA at 11:35, 20 October 2012

OCA — Sat, 20 Oct 2012 11:35:21 GMT

←Older revision		Revision as of 11:35, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3it9]] is a 4 chain structure ~~of [[Carboxypeptidase]] and [[Penicillin-binding protein]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA].	+	[[3it9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA].

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

OCA: Protected "3it9" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 05:53:30 GMT

Protected "3it9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:53, 26 July 2012

OCA at 05:53, 26 July 2012

OCA — Thu, 26 Jul 2012 05:53:28 GMT

←Older revision		Revision as of 05:53, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3it9.png\|left\|200px]]		[[Image:3it9.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3it9", 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_3it9\| PDB=3it9 \| SCENE= }}		{{STRUCTURE_3it9\| PDB=3it9 \| SCENE= }}

	===Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state===		===Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19807181}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19807181 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19807181}}		{{ABSTRACT_PUBMED_19807181}}

	==About this Structure==		==About this Structure==
-	~~3IT9~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/~~Thermomicrobium_roseum Thermomicrobium roseum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA].	+	[[3it9]] is a 4 chain structure of [[Carboxypeptidase]] and [[Penicillin-binding protein]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA].
		+
		+	==See Also==
		+	*[[Carboxypeptidase\|Carboxypeptidase]]
		+	*[[Penicillin-binding protein\|Penicillin-binding protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19807181~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019807181</ref><references group="xtra"/>
		+	[[Category: Escherichia coli]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: Thermomicrobium roseum]]
	[[Category: Chen, Y.]]		[[Category: Chen, Y.]]
	[[Category: Hesek, D.]]		[[Category: Hesek, D.]]
Line 46:		Line 38:
	[[Category: Peptidoglycan synthesis]]		[[Category: Peptidoglycan synthesis]]
	[[Category: Protease]]		[[Category: Protease]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 12 00:00:36 2009''

OCA at 22:00, 11 November 2009

OCA — Wed, 11 Nov 2009 22:00:40 GMT

←Older revision		Revision as of 22:00, 11 November 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3it9.~~jpg~~\|left\|200px]]	+	[[Image:3it9.png\|left\|200px]]

	<!--		<!--
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3IT9 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA].	+	3IT9 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermomicrobium_roseum Thermomicrobium roseum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:19807181</ref><references group="xtra"/>		<ref group="xtra">PMID:19807181</ref><references group="xtra"/>
-	[[Category: Escherichia coli]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
		+	[[Category: Thermomicrobium roseum]]
	[[Category: Chen, Y.]]		[[Category: Chen, Y.]]
	[[Category: Hesek, D.]]		[[Category: Hesek, D.]]
Line 47:		Line 47:
	[[Category: Protease]]		[[Category: Protease]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Oct 21 10~~:23:21 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 12 00:00:36 2009''