5nf0 - Revision history

OCA at 12:52, 15 November 2023

OCA — Wed, 15 Nov 2023 12:52:10 GMT

←Older revision		Revision as of 12:52, 15 November 2023
Line 1:		Line 1:

	==Discovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa==		==Discovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa==
-	<StructureSection load='5nf0' size='340' side='right' caption='[[5nf0]], [[Resolution\|resolution]] 1.27Å' scene=''>	+	<StructureSection load='5nf0' size='340' side='right'caption='[[5nf0]], [[Resolution\|resolution]] 1.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nf0]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NF0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NF0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nf0]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NF0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NF0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'~~>~~CA</scene>, <scene name='pdbligand=OXE:ORTHO~~-~~XYLENE'>OXE</scene>~~, ~~<scene name='pdbligand=ZDC:3,7-ANHYDRO-2,8-DIDEOXY-L-GLYCERO-D-GLUCO-OCTONIC+ACID'>ZDC</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.271Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=DTR:D-TRYPTOPHAN'>DTR</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=DTR:D-TRYPTOPHAN'>DTR</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=OXE:ORTHO-XYLENE'>OXE</scene>, <scene name='pdbligand=ZDC:3,7-ANHYDRO-2,8-DIDEOXY-L-GLYCERO-D-GLUCO-OCTONIC+ACID'>ZDC</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">lecB, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=5nf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nf0 OCA], [https://pdbe.org/5nf0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nf0 RCSB], [https://www.ebi.ac.uk/pdbsum/5nf0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nf0 ProSAT]</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=5nf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nf0 OCA], [~~http~~://pdbe.org/5nf0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nf0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nf0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nf0 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9HYN5_PSEAE Q9HYN5_PSEAE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bonaventura, I Di]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Darbre, T]]~~	+
-	~~[[Category: Delden, C van]]~~	+
-	~~[[Category: Fu, Y]]~~	+
-	~~[[Category: He, R]]~~	+
-	~~[[Category: Hong, W]]~~	+
-	~~[[Category: Koehler, T]]~~	+
-	~~[[Category: Luscher, A]]~~	+
-	~~[[Category: Reymond, J L]]~~	+
-	~~[[Category: Stocker, A]]~~	+
-	~~[[Category: Visini, R]]~~	+
-	~~[[Category: Antimicrobial protein]]~~	+
-	~~[[Category: Antimicrobial]]~~	+
-	~~[[Category: Cyclic peptide~~]]	+
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Darbre T]]
		+	[[Category: Di Bonaventura I]]
		+	[[Category: Fu Y]]
		+	[[Category: He R]]
		+	[[Category: Hong W]]
		+	[[Category: Koehler T]]
		+	[[Category: Luscher A]]
		+	[[Category: Reymond J-L]]
		+	[[Category: Stocker A]]
		+	[[Category: Visini R]]
		+	[[Category: Van Delden C]]

OCA at 07:42, 6 December 2017

OCA — Wed, 06 Dec 2017 07:42:28 GMT

←Older revision		Revision as of 07:42, 6 December 2017
Line 3:		Line 3:
	<StructureSection load='5nf0' size='340' side='right' caption='[[5nf0]], [[Resolution\|resolution]] 1.27Å' scene=''>		<StructureSection load='5nf0' size='340' side='right' caption='[[5nf0]], [[Resolution\|resolution]] 1.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nf0]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NF0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NF0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nf0]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NF0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NF0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=OXE:ORTHO-XYLENE'>OXE</scene>, <scene name='pdbligand=ZDC:3,7-ANHYDRO-2,8-DIDEOXY-L-GLYCERO-D-GLUCO-OCTONIC+ACID'>ZDC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=OXE:ORTHO-XYLENE'>OXE</scene>, <scene name='pdbligand=ZDC:3,7-ANHYDRO-2,8-DIDEOXY-L-GLYCERO-D-GLUCO-OCTONIC+ACID'>ZDC</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=DTR:D-TRYPTOPHAN'>DTR</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=DTR:D-TRYPTOPHAN'>DTR</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lecB, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=5nf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nf0 OCA], [http://pdbe.org/5nf0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nf0 RCSB], [http://www.ebi.ac.uk/pdbsum/5nf0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nf0 ProSAT]</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=5nf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nf0 OCA], [http://pdbe.org/5nf0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nf0 RCSB], [http://www.ebi.ac.uk/pdbsum/5nf0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nf0 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Here we report a new family of cyclic antimicrobial peptides (CAMPs) targeting MDR strains of Pseudomonas aeruginosa. These CAMPs are cyclized via a xylene double thioether bridge connecting two cysteines placed at the ends of a linear amphiphilic alternating d,l-sequence composed of lysines and tryptophans. Investigations by transmission electron microscopy (TEM), dynamic light scattering and atomic force microscopy (AFM) suggest that these peptide macrocycles interact with the membrane to form lipid-peptide aggregates. Amphiphilic conformations compatible with membrane disruption are observed in high resolution X-ray crystal structures of fucosylated derivatives in complex with lectin LecB. The potential for optimization is highlighted by N-methylation of backbone amides leading to derivatives with similar antimicrobial activity but lower hemolysis.
		+
		+	Design, crystal structure and atomic force microscopy study of thioether ligated d,l-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa.,He R, Di Bonaventura I, Visini R, Gan BH, Fu Y, Probst D, Luscher A, Kohler T, van Delden C, Stocker A, Hong W, Darbre T, Reymond JL Chem Sci. 2017 Nov 1;8(11):7464-7475. doi: 10.1039/c7sc01599b. Epub 2017 Sep 4. PMID:29163899<ref>PMID:29163899</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5nf0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:22, 6 October 2017

OCA — Fri, 06 Oct 2017 05:22:45 GMT

←Older revision		Revision as of 05:22, 6 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5nf0 is ~~ON HOLD until Paper Publication~~	+	==Discovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa==
-		+	<StructureSection load='5nf0' size='340' side='right' caption='[[5nf0]], [[Resolution\|resolution]] 1.27Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5nf0]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NF0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NF0 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=OXE:ORTHO-XYLENE'>OXE</scene>, <scene name='pdbligand=ZDC:3,7-ANHYDRO-2,8-DIDEOXY-L-GLYCERO-D-GLUCO-OCTONIC+ACID'>ZDC</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=DTR:D-TRYPTOPHAN'>DTR</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></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=5nf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nf0 OCA], [http://pdbe.org/5nf0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nf0 RCSB], [http://www.ebi.ac.uk/pdbsum/5nf0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nf0 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bonaventura, I Di]]
		+	[[Category: Darbre, T]]
		+	[[Category: Delden, C van]]
		+	[[Category: Fu, Y]]
		+	[[Category: He, R]]
		+	[[Category: Hong, W]]
		+	[[Category: Koehler, T]]
		+	[[Category: Luscher, A]]
		+	[[Category: Reymond, J L]]
		+	[[Category: Stocker, A]]
		+	[[Category: Visini, R]]
		+	[[Category: Antimicrobial protein]]
		+	[[Category: Antimicrobial]]
		+	[[Category: Cyclic peptide]]
		+	[[Category: Pseudomonas aeruginosa]]

OCA at 09:26, 19 April 2017

OCA — Wed, 19 Apr 2017 09:26:23 GMT

←Older revision		Revision as of 09:26, 19 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5nf0 is ON HOLD	+	The entry 5nf0 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5nf0" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 09:58:14 GMT

Protected "5nf0" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:58, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5nf0 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Apr 2017 09:58:13 GMT

New page: '''Unreleased structure''' The entry 5nf0 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5nf0 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]