6s5p - Revision history

OCA at 12:35, 24 January 2024

OCA — Wed, 24 Jan 2024 12:35:50 GMT

←Older revision		Revision as of 12:35, 24 January 2024
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	<StructureSection load='6s5p' size='340' side='right'caption='[[6s5p]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='6s5p' size='340' side='right'caption='[[6s5p]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6s5p]] is a 7 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=6S5P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6S5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s5p]] is a 7 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=6S5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S5P 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]] 1.46Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><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=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, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453 ([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=6s5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s5p OCA], [https://pdbe.org/6s5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s5p RCSB], [https://www.ebi.ac.uk/pdbsum/6s5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s5p 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=6s5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s5p OCA], [~~http~~://pdbe.org/6s5p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6s5p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6s5p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6s5p 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 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Baeriswyl, S~~]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Reymond, J L~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Stocker, A~~]]	+	[[Category: Baeriswyl S]]
-	[[Category: ~~Fucosylated~~]]	+	[[Category: Reymond J-L]]
-	[[Category: ~~Lectin]]~~	+	[[Category: Stocker A]]
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 16:08, 28 August 2019

OCA — Wed, 28 Aug 2019 16:08:56 GMT

←Older revision		Revision as of 16:08, 28 August 2019
Line 3:		Line 3:
	<StructureSection load='6s5p' size='340' side='right'caption='[[6s5p]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='6s5p' size='340' side='right'caption='[[6s5p]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6s5p]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6S5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s5p]] is a 7 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=6S5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6S5P 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=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=NH2:AMINO+GROUP'>NH2</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453 ([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=6s5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s5p OCA], [http://pdbe.org/6s5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s5p RCSB], [http://www.ebi.ac.uk/pdbsum/6s5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s5p 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=6s5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s5p OCA], [http://pdbe.org/6s5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s5p RCSB], [http://www.ebi.ac.uk/pdbsum/6s5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s5p ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Herein, we report X-ray crystal structures of 11-13 residue antimicrobial peptides (AMPs) active against Pseudomonas aeruginosa as complexes of fucosylated d-enantiomeric sequences with the P. aeruginosa lectin LecB. These represent the first crystal structures of short AMPs. In 24 individual structures of eight different peptides, we found mostly alpha-helices assembled as two-helix or four-helix bundles with a hydrophobic core and cationic residues pointing outside. Two of the analogs formed an extended structure engaging in multiple contacts with the lectin. Molecular dynamics (MD) simulations showed that alpha-helices are stabilized by bundle formation and suggested that the N-terminal acyl group present in the linker to the fucosyl group can extend the helix by one additional H-bond and increase alpha-helix amphiphilicity. Investigating N-terminal acylation led to AMPs with equivalent and partly stronger antibacterial effects compared to the free peptide.
		+
		+	X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes.,Baeriswyl S, Gan BH, Siriwardena TN, Visini R, Robadey M, Javor S, Stocker A, Darbre T, Reymond JL ACS Chem Biol. 2019 Mar 11. doi: 10.1021/acschembio.9b00047. PMID:30830745<ref>PMID:30830745</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6s5p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:13, 21 August 2019

OCA — Wed, 21 Aug 2019 06:13:49 GMT

←Older revision		Revision as of 06:13, 21 August 2019
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-	'''Unreleased structure'''

-	~~The entry 6s5p is ON HOLD until Paper Publication~~	+	==Cfucosylated peptide SBL2 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.46 Angstrom resolution==
-		+	<StructureSection load='6s5p' size='340' side='right'caption='[[6s5p]], [[Resolution\|resolution]] 1.46Å' scene=''>
-	~~Authors: Baeriswyl, S., Stocker, A., Reymond, J.-L.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6s5p]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6S5P FirstGlance]. <br>
-	~~Description:~~ Cfucosylated peptide SBL2 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.46 Angstrom resolution	+	</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=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-	[[~~Category~~: ~~Reymond~~, J.-L]]	+	<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=6s5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s5p OCA], [http://pdbe.org/6s5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s5p RCSB], [http://www.ebi.ac.uk/pdbsum/6s5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s5p ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Baeriswyl, S]]		[[Category: Baeriswyl, S]]
		+	[[Category: Reymond, J L]]
	[[Category: Stocker, A]]		[[Category: Stocker, A]]
		+	[[Category: Fucosylated]]
		+	[[Category: Lectin]]
		+	[[Category: Sugar binding protein]]

OCA at 09:14, 17 July 2019

OCA — Wed, 17 Jul 2019 09:14:14 GMT

←Older revision		Revision as of 09:14, 17 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6s5p is ON HOLD	+	The entry 6s5p is ON HOLD until Paper Publication

	Authors: Baeriswyl, S., Stocker, A., Reymond, J.-L.		Authors: Baeriswyl, S., Stocker, A., Reymond, J.-L.

-	Description: Cfucosylated peptide ~~SB58~~ bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.46 Angstrom resolution	+	Description: Cfucosylated peptide SBL2 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.46 Angstrom resolution
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Reymond, J.-L]]		[[Category: Reymond, J.-L]]
	[[Category: Baeriswyl, S]]		[[Category: Baeriswyl, S]]
	[[Category: Stocker, A]]		[[Category: Stocker, A]]

OCA: Protected "6s5p" [edit=sysop:move=sysop]

OCA — Wed, 10 Jul 2019 04:26:15 GMT

Protected "6s5p" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:26, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6s5p is ON HOLD Authors: Baeriswyl, S., Stocker, A., Reymond, J.-L. Description: Cfucosylated peptide SB58 bound to Fucose binding Lectin LecB (PA-...

OCA — Wed, 10 Jul 2019 04:26:14 GMT

New page: '''Unreleased structure''' The entry 6s5p is ON HOLD Authors: Baeriswyl, S., Stocker, A., Reymond, J.-L. Description: Cfucosylated peptide SB58 bound to Fucose binding Lectin LecB (PA-...

New page

'''Unreleased structure'''

The entry 6s5p is ON HOLD

Authors: Baeriswyl, S., Stocker, A., Reymond, J.-L.

Description: Cfucosylated peptide SB58 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.46 Angstrom resolution
[[Category: Unreleased Structures]]
[[Category: Reymond, J.-L]]
[[Category: Baeriswyl, S]]
[[Category: Stocker, A]]