3td5 - Revision history

OCA at 17:31, 1 November 2023

2023-11-01T17:31:23Z

←Older revision		Revision as of 17:31, 1 November 2023
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	<StructureSection load='3td5' size='340' side='right'caption='[[3td5]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3td5' size='340' side='right'caption='[[3td5]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3td5]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aciba Aciba~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TD5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3td5]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TD5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3td3\|3td3]], [[3td4\|3td4]]</div></td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">omp38 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])~~</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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [https://pdbe.org/3td5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [https://www.ebi.ac.uk/pdbsum/3td5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3td5 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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [https://pdbe.org/3td5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [https://www.ebi.ac.uk/pdbsum/3td5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3td5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~OMP38_ACIBA OMP38_ACIBA~~]~~] Porin~~. Induces apoptosis in human ~~laryngeal epithelial HEp-2 cells~~ through ~~caspases~~-dependent and AIF-dependent pathways. Purified Omp38 enters ~~the cells~~ and localizes to the mitochondria, which leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor).<ref>PMID:16008580</ref> <ref>PMID:9928952</ref>	+	[https://www.uniprot.org/uniprot/OMP38_ACIB2 OMP38_ACIB2] Functions as a porin (PubMed:9928952). Induces apoptosis in human cell lines through caspase-dependent and AIF-dependent pathways. Purified Omp38 enters host cell and localizes to the mitochondria, which presumably leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor) (PubMed:16008580). Binds peptidoglycan, contributes to cell wall maintenance (Probable).<ref>PMID:16008580</ref> <ref>PMID:9928952</ref> <ref>PMID:16008580</ref> <ref>PMID:21965596</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aciba~~]]	+	[[Category: Acinetobacter baumannii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim~~, H Y~~]]	+	[[Category: Kim HY]]
-	[[Category: Lee~~, W C~~]]	+	[[Category: Lee WC]]
-	[[Category: Park~~, J S~~]]	+	[[Category: Park JS]]
-	[[Category: Song~~, J H]]~~	+	[[Category: Song JH]]
-	~~[[Category: Cell-wall attachment]]~~	+
-	~~[[Category: Membrane protein-peptide binding protein complex]]~~	+
-	~~[[Category: Ompa-like fold]]~~	+
-	~~[[Category: Peptidoglycan-binding~~]]	+

OCA at 16:52, 6 July 2022

2022-07-06T16:52:53Z

←Older revision		Revision as of 16:52, 6 July 2022
Line 1:		Line 1:

	==Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala==		==Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala==
-	<StructureSection load='3td5' size='340' side='right' caption='[[3td5]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3td5' size='340' side='right'caption='[[3td5]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3td5]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aciba Aciba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TD5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3td5]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Aciba Aciba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TD5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3td3\|3td3]], [[3td4\|3td4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3td3\|3td3]], [[3td4\|3td4]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">omp38 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">omp38 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])</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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [~~http~~://pdbe.org/3td5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3td5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3td5 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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [https://pdbe.org/3td5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [https://www.ebi.ac.uk/pdbsum/3td5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3td5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/OMP38_ACIBA OMP38_ACIBA]] Porin. Induces apoptosis in human laryngeal epithelial HEp-2 cells through caspases-dependent and AIF-dependent pathways. Purified Omp38 enters the cells and localizes to the mitochondria, which leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor).<ref>PMID:16008580</ref> <ref>PMID:9928952</ref>	+	[[https://www.uniprot.org/uniprot/OMP38_ACIBA OMP38_ACIBA]] Porin. Induces apoptosis in human laryngeal epithelial HEp-2 cells through caspases-dependent and AIF-dependent pathways. Purified Omp38 enters the cells and localizes to the mitochondria, which leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor).<ref>PMID:16008580</ref> <ref>PMID:9928952</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Aciba]]		[[Category: Aciba]]
		+	[[Category: Large Structures]]
	[[Category: Kim, H Y]]		[[Category: Kim, H Y]]
	[[Category: Lee, W C]]		[[Category: Lee, W C]]

OCA at 17:00, 5 August 2016

2016-08-05T17:00:01Z

←Older revision		Revision as of 17:00, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala==		==Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala==
	<StructureSection load='3td5' size='340' side='right' caption='[[3td5]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3td5' size='340' side='right' caption='[[3td5]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3td5]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Acinetobacter_baumannii Acinetobacter baumannii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TD5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3td5]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciba Aciba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TD5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3td3\|3td3]], [[3td4\|3td4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3td3\|3td3]], [[3td4\|3td4]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">omp38 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ~~Acinetobacter baumannii~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">omp38 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])</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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [http://www.ebi.ac.uk/pdbsum/3td5 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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [http://pdbe.org/3td5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [http://www.ebi.ac.uk/pdbsum/3td5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3td5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 3td5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acinetobacter baumannii~~]]	+	[[Category: Aciba]]
	[[Category: Kim, H Y]]		[[Category: Kim, H Y]]
	[[Category: Lee, W C]]		[[Category: Lee, W C]]

OCA at 04:14, 25 December 2014

2014-12-25T04:14:18Z

←Older revision		Revision as of 04:14, 25 December 2014
Line 9:		Line 9:
	<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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [http://www.ebi.ac.uk/pdbsum/3td5 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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [http://www.ebi.ac.uk/pdbsum/3td5 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/OMP38_ACIBA OMP38_ACIBA]] Porin. Induces apoptosis in human laryngeal epithelial HEp-2 cells through caspases-dependent and AIF-dependent pathways. Purified Omp38 enters the cells and localizes to the mitochondria, which leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor).<ref>PMID:16008580</ref> <ref>PMID:9928952</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 06:37, 21 December 2014

2014-12-21T06:37:23Z

←Older revision		Revision as of 06:37, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3td5\| PDB=3td5 \| SCENE= }}~~	+	==Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala==
-	===Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala===	+	<StructureSection load='3td5' size='340' side='right' caption='[[3td5]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21965596}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3td5]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TD5 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3td3\|3td3]], [[3td4\|3td4]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">omp38 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 Acinetobacter baumannii])</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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [http://www.ebi.ac.uk/pdbsum/3td5 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The outer membrane protein A (OmpA) plays important roles in anchoring of the outer membrane to the bacterial cell wall. The C-terminal periplasmic domain of OmpA (OmpA-like domain) associates with the peptidoglycan (PGN) layer noncovalently. However, there is a paucity of information on the structural aspects of the mechanism of PGN recognition by OmpA-like domains. To elucidate this molecular recognition process, we solved the high-resolution crystal structure of an OmpA-like domain from Acinetobacter baumannii bound to diaminopimelate (DAP), a unique bacterial amino acid from the PGN. The structure clearly illustrates that two absolutely conserved Asp271 and Arg286 residues are the key to the binding to DAP of PGN. Identification of DAP as the central anchoring site of PGN to OmpA is further supported by isothermal titration calorimetry and a pulldown assay with PGN. An NMR-based computational model for complexation between the PGN and OmpA emerged, and this model is validated by determining the crystal structure in complex with a synthetic PGN fragment. These structural data provide a detailed glimpse of how the anchoring of OmpA to the cell wall of gram-negative bacteria takes place in a DAP-dependent manner.-Park, J. S., Lee, W. C., Yeo, K. J., Ryu, K.-S., Kumarasiri, M., Hesek, D., Lee, M., Mobashery, S., Song, J. H., Lim, S. I., Lee, J. C., Cheong, C., Jeon, Y. H., Kim, H.-Y. Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram-negative bacterial outer membrane.

-	~~==Function==~~	+	Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram-negative bacterial outer membrane.,Park JS, Lee WC, Yeo KJ, Ryu KS, Kumarasiri M, Hesek D, Lee M, Mobashery S, Song JH, Kim SI, Lee JC, Cheong C, Jeon YH, Kim HY FASEB J. 2011 Sep 30. PMID:21965596<ref>PMID:21965596</ref>
-	[[http://www.uniprot.org/uniprot/OMP38_ACIBA OMP38_ACIBA]] Porin. Induces apoptosis in human laryngeal epithelial HEp-2 cells through caspases-dependent and AIF-dependent pathways. Purified Omp38 enters the cells and localizes to the ~~mitochondria, which leads to a release~~ of ~~proapoptotic molecules such as cytochrome c and AIF (apoptosis~~-~~inducing factor)~~.~~<ref>~~PMID:~~16008580</ref>~~ <ref>PMID:~~9928952~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3td5]] is~~ a ~~16 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:021965596</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Acinetobacter baumannii]]		[[Category: Acinetobacter baumannii]]
-	[[Category: Kim, H Y.]]	+	[[Category: Kim, H Y]]
-	[[Category: Lee, W C.]]	+	[[Category: Lee, W C]]
-	[[Category: Park, J S.]]	+	[[Category: Park, J S]]
-	[[Category: Song, J H.]]	+	[[Category: Song, J H]]
	[[Category: Cell-wall attachment]]		[[Category: Cell-wall attachment]]
	[[Category: Membrane protein-peptide binding protein complex]]		[[Category: Membrane protein-peptide binding protein complex]]
	[[Category: Ompa-like fold]]		[[Category: Ompa-like fold]]
	[[Category: Peptidoglycan-binding]]		[[Category: Peptidoglycan-binding]]

OCA at 07:11, 30 June 2013

2013-06-30T07:11:42Z

←Older revision		Revision as of 07:11, 30 June 2013
Line 1:		Line 1:
-	[[Image:3td5.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3td5", 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_3td5\| PDB=3td5 \| SCENE= }}		{{STRUCTURE_3td5\| PDB=3td5 \| SCENE= }}
-
	===Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala===		===Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala===
		+	{{ABSTRACT_PUBMED_21965596}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/OMP38_ACIBA OMP38_ACIBA]] Porin. Induces apoptosis in human laryngeal epithelial HEp-2 cells through caspases-dependent and AIF-dependent pathways. Purified Omp38 enters the cells and localizes to the mitochondria, which leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor).<ref>PMID:16008580</ref> <ref>PMID:9928952</ref>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21965596}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 21965596 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_21965596}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:021965596</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021965596</ref><references group="xtra"/><references/>
	[[Category: Acinetobacter baumannii]]		[[Category: Acinetobacter baumannii]]
	[[Category: Kim, H Y.]]		[[Category: Kim, H Y.]]

OCA at 09:21, 30 October 2011

2011-10-30T09:21:21Z

←Older revision		Revision as of 09:21, 30 October 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3td5.png\|left\|200px]]

-	The ~~entry 3td5~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3td5", 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_3td5\| PDB=3td5 \| SCENE= }}

-	~~Authors: Park, J.S., Lee, W.C., Song, J.H., Kim, H.Y.~~	+	===Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala===

-	~~Description~~: ~~Crystal structure of OmpA~~-~~like domain~~ from Acinetobacter baumannii ~~in complex with L~~-~~Ala~~-~~gamma~~-~~D-Glu~~-~~m-DAP-D-Ala-D~~-~~Ala~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21965596}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21965596 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21965596}}
		+
		+	==About this Structure==
		+	[[3td5]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021965596</ref><references group="xtra"/>
		+	[[Category: Acinetobacter baumannii]]
		+	[[Category: Kim, H Y.]]
		+	[[Category: Lee, W C.]]
		+	[[Category: Park, J S.]]
		+	[[Category: Song, J H.]]
		+	[[Category: Cell-wall attachment]]
		+	[[Category: Membrane protein-peptide binding protein complex]]
		+	[[Category: Ompa-like fold]]
		+	[[Category: Peptidoglycan-binding]]

OCA at 06:08, 5 October 2011

2011-10-05T06:08:17Z

←Older revision		Revision as of 06:08, 5 October 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3td5 is ON HOLD	+	The entry 3td5 is ON HOLD until Paper Publication

	Authors: Park, J.S., Lee, W.C., Song, J.H., Kim, H.Y.		Authors: Park, J.S., Lee, W.C., Song, J.H., Kim, H.Y.

	Description: Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala		Description: Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala

OCA at 06:03, 14 September 2011

2011-09-14T06:03:16Z

←Older revision		Revision as of 06:03, 14 September 2011
Line 5:		Line 5:
	Authors: Park, J.S., Lee, W.C., Song, J.H., Kim, H.Y.		Authors: Park, J.S., Lee, W.C., Song, J.H., Kim, H.Y.

-	Description: ~~Mechanism~~ of ~~Anchoring of the Cell Wall Peptidoglycan to~~ OmpA ~~Protein of the Gram~~-~~Negative Bacterial Outer Membrane~~	+	Description: Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala

OCA: Protected "3td5" [edit=sysop:move=sysop]

2011-08-17T05:57:53Z

Protected "3td5" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:57, 17 August 2011