5i8x - Revision history

OCA at 08:27, 23 August 2023

2023-08-23T08:27:09Z

←Older revision		Revision as of 08:27, 23 August 2023
Line 1:		Line 1:

	==Bicyclic antimibrocial peptides==		==Bicyclic antimibrocial peptides==
-	<StructureSection load='5i8x' size='340' side='right' caption='[[5i8x]], [[Resolution\|resolution]] 1.89Å' scene=''>	+	<StructureSection load='5i8x' size='340' side='right'caption='[[5i8x]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i8x]] is a 5 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=5I8X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I8X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i8x]] is a 5 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=5I8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I8X 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=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]] 1.89Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=DLS:DI-ACETYL-LYSINE'>DLS</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=DLS:DI-ACETYL-LYSINE'>DLS</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</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, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AN451_21855, AN453_22575, AN455_18155, AN456_19070, AN457_11175, AN458_15745, AN460_27980, AN462_17515, AOD73_08535, AOX61_23230, AOX62_26425, APG03_22020, APG04_23970, APG05_03535, APG06_28020, APG07_27985, ATC05_02360, ERS445055_01627, PA8380_17510, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713, PAO1OR1608 ([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=5i8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8x OCA], [https://pdbe.org/5i8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i8x RCSB], [https://www.ebi.ac.uk/pdbsum/5i8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8x 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=5i8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8x OCA], [~~http~~://pdbe.org/5i8x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i8x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i8x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8x 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: Jin, X]]~~	+
-	~~[[Category: Koehler, T]]~~	+
-	~~[[Category: Michaud, G]]~~	+
-	~~[[Category: Reymond, J L]]~~	+
-	~~[[Category: Robadey, M]]~~	+
-	~~[[Category: Stocker, A]]~~	+
-	~~[[Category: Visini, R]]~~	+
-	~~[[Category: Antimicrobial peptide]]~~	+
-	~~[[Category: Bicycle]]~~	+
-	~~[[Category: Biofilm~~]]	+
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Sugar binding protein~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: Darbre T]]
		+	[[Category: Di Bonaventura I]]
		+	[[Category: Jin X]]
		+	[[Category: Koehler T]]
		+	[[Category: Michaud G]]
		+	[[Category: Reymond J-L]]
		+	[[Category: Robadey M]]
		+	[[Category: Stocker A]]
		+	[[Category: Visini R]]
		+	[[Category: Van Delden C]]

OCA at 07:24, 29 November 2017

2017-11-29T07:24:31Z

←Older revision		Revision as of 07:24, 29 November 2017
Line 3:		Line 3:
	<StructureSection load='5i8x' size='340' side='right' caption='[[5i8x]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='5i8x' size='340' side='right' caption='[[5i8x]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i8x]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i8x]] is a 5 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=5I8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8X 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=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=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=DLS:DI-ACETYL-LYSINE'>DLS</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=DLS:DI-ACETYL-LYSINE'>DLS</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, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AN451_21855, AN453_22575, AN455_18155, AN456_19070, AN457_11175, AN458_15745, AN460_27980, AN462_17515, AOD73_08535, AOX61_23230, AOX62_26425, APG03_22020, APG04_23970, APG05_03535, APG06_28020, APG07_27985, ATC05_02360, ERS445055_01627, PA8380_17510, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713, PAO1OR1608 ([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=5i8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8x OCA], [http://pdbe.org/5i8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8x RCSB], [http://www.ebi.ac.uk/pdbsum/5i8x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8x 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=5i8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8x OCA], [http://pdbe.org/5i8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8x RCSB], [http://www.ebi.ac.uk/pdbsum/5i8x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8x ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Herein we report the discovery of antimicrobial bridged bicyclic peptides (AMBPs) active against Pseudomonas aeruginosa, a highly problematic Gram negative bacterium in the hospital environment. Two of these AMBPs show strong biofilm inhibition and dispersal activity and enhance the activity of polymyxin, currently a last resort antibiotic against which resistance is emerging. To discover our AMBPs we used the concept of chemical space, which is well known in the area of small molecule drug discovery, to define a small number of test compounds for synthesis and experimental evaluation. Our chemical space was calculated using 2DP, a new topological shape and pharmacophore fingerprint for peptides. This method provides a general strategy to search for bioactive peptides with unusual topologies and expand the structural diversity of peptide-based drugs.
		+
		+	Chemical space guided discovery of antimicrobial bridged bicyclic peptides against Pseudomonas aeruginosa and its biofilms.,Di Bonaventura I, Jin X, Visini R, Probst D, Javor S, Gan BH, Michaud G, Natalello A, Doglia SM, Kohler T, van Delden C, Stocker A, Darbre T, Reymond JL Chem Sci. 2017 Oct 1;8(10):6784-6798. doi: 10.1039/c7sc01314k. Epub 2017 Jul 13. PMID:29147502<ref>PMID:29147502</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5i8x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:02, 6 October 2017

2017-10-06T07:02:58Z

←Older revision		Revision as of 07:02, 6 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i8x ~~is ON HOLD until Paper Publication~~	+	==Bicyclic antimibrocial peptides==
-		+	<StructureSection load='5i8x' size='340' side='right' caption='[[5i8x]], [[Resolution\|resolution]] 1.89Å' scene=''>
-	~~Authors~~: ~~Di Bonaventura, I~~.~~, Jin, X~~.~~, Visini, R~~.~~, Michaud, G~~.~~, Robadey, M~~.~~, Koehler, T~~.~~, van Delden, C~~.~~, Stocker, A~~.~~, Darbre, T~~., ~~Reymond~~, J.-L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5i8x]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8X FirstGlance]. <br>
-	~~Description: Bicyclic antimibrocial peptides~~	+	</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=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=DLS:DI-ACETYL-LYSINE'>DLS</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-	[[~~Category~~: ~~Visini~~, R]]	+	<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=5i8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8x OCA], [http://pdbe.org/5i8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8x RCSB], [http://www.ebi.ac.uk/pdbsum/5i8x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8x ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Reymond~~, J.-L]]	+	</table>
-	[[Category: ~~Robadey~~, M]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Bonaventura, I Di]]
	[[Category: Darbre, T]]		[[Category: Darbre, T]]
-	[[Category: ~~Stocker~~, A]]	+	[[Category: Delden, C van]]
	[[Category: Jin, X]]		[[Category: Jin, X]]
		+	[[Category: Koehler, T]]
	[[Category: Michaud, G]]		[[Category: Michaud, G]]
-	[[Category: ~~Van Delden~~, C]]	+	[[Category: Reymond, J L]]
-	[[Category: ~~Koehler~~, T]]	+	[[Category: Robadey, M]]
-	[[Category: ~~Di Bonaventura~~, I]]	+	[[Category: Stocker, A]]
		+	[[Category: Visini, R]]
		+	[[Category: Antimicrobial peptide]]
		+	[[Category: Bicycle]]
		+	[[Category: Biofilm]]
		+	[[Category: Pseudomonas aeruginosa]]
		+	[[Category: Sugar binding protein]]

OCA at 09:33, 9 March 2017

2017-03-09T09:33:21Z

←Older revision		Revision as of 09:33, 9 March 2017
Line 7:		Line 7:
	Description: Bicyclic antimibrocial peptides		Description: Bicyclic antimibrocial peptides
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Robadey, M]]
-	[[Category: Michaud, G]]
-	[[Category: Koehler, T]]
	[[Category: Visini, R]]		[[Category: Visini, R]]
	[[Category: Reymond, J.-L]]		[[Category: Reymond, J.-L]]
		+	[[Category: Robadey, M]]
	[[Category: Darbre, T]]		[[Category: Darbre, T]]
	[[Category: Stocker, A]]		[[Category: Stocker, A]]
	[[Category: Jin, X]]		[[Category: Jin, X]]
		+	[[Category: Michaud, G]]
	[[Category: Van Delden, C]]		[[Category: Van Delden, C]]
		+	[[Category: Koehler, T]]
	[[Category: Di Bonaventura, I]]		[[Category: Di Bonaventura, I]]

OCA at 00:18, 11 May 2016

2016-05-11T00:18:03Z

←Older revision		Revision as of 00:18, 11 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i8x is ON HOLD	+	The entry 5i8x is ON HOLD until Paper Publication

	Authors: Di Bonaventura, I., Jin, X., Visini, R., Michaud, G., Robadey, M., Koehler, T., van Delden, C., Stocker, A., Darbre, T., Reymond, J.-L.		Authors: Di Bonaventura, I., Jin, X., Visini, R., Michaud, G., Robadey, M., Koehler, T., van Delden, C., Stocker, A., Darbre, T., Reymond, J.-L.

OCA: Protected "5i8x" [edit=sysop:move=sysop]

2016-03-02T13:32:49Z

Protected "5i8x" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:32, 2 March 2016

OCA: New page: '''Unreleased structure''' The entry 5i8x is ON HOLD Authors: Di Bonaventura, I., Jin, X., Visini, R., Michaud, G., Robadey, M., Koehler, T., van Delden, C., Stocker, A., Darbre, T., Re...

2016-03-02T13:32:48Z

New page: '''Unreleased structure''' The entry 5i8x is ON HOLD Authors: Di Bonaventura, I., Jin, X., Visini, R., Michaud, G., Robadey, M., Koehler, T., van Delden, C., Stocker, A., Darbre, T., Re...

New page

'''Unreleased structure'''

The entry 5i8x is ON HOLD

Authors: Di Bonaventura, I., Jin, X., Visini, R., Michaud, G., Robadey, M., Koehler, T., van Delden, C., Stocker, A., Darbre, T., Reymond, J.-L.

Description: Bicyclic antimibrocial peptides
[[Category: Unreleased Structures]]
[[Category: Robadey, M]]
[[Category: Michaud, G]]
[[Category: Koehler, T]]
[[Category: Visini, R]]
[[Category: Reymond, J.-L]]
[[Category: Darbre, T]]
[[Category: Stocker, A]]
[[Category: Jin, X]]
[[Category: Van Delden, C]]
[[Category: Di Bonaventura, I]]