6y0v - Revision history

OCA at 07:50, 7 February 2024

OCA — Wed, 07 Feb 2024 07:50:26 GMT

←Older revision		Revision as of 07:50, 7 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6y0v]] 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=6Y0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y0V FirstGlance]. <br>		<table><tr><td colspan='2'>[[6y0v]] 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=6Y0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y0V FirstGlance]. <br>
-	</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=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=O65:3,5-bis(hydroxymethyl)-4-methyl-benzaldehyde'>O65</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]] 1.98Å</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=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=O65:3,5-bis(hydroxymethyl)-4-methyl-benzaldehyde'>O65</scene>, <scene name='pdbligand=ZDC:3,7-ANHYDRO-2,8-DIDEOXY-L-GLYCERO-D-GLUCO-OCTONIC+ACID'>ZDC</scene></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=6y0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0v OCA], [https://pdbe.org/6y0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y0v RCSB], [https://www.ebi.ac.uk/pdbsum/6y0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0v 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=6y0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0v OCA], [https://pdbe.org/6y0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y0v RCSB], [https://www.ebi.ac.uk/pdbsum/6y0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q9HYN5_PSEAE Q9HYN5_PSEAE]		[https://www.uniprot.org/uniprot/Q9HYN5_PSEAE Q9HYN5_PSEAE]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The peptide alpha-helix is right-handed when containing amino acids with l-chirality, and left-handed with d-chirality, however mixed chirality peptides generally do not form alpha-helices unless a helix inducer such as the non-natural residue amino-isobutyric acid is used. Herein we report the first X-ray crystal structures of mixed chirality alpha-helices in short peptides comprising only natural residues as the example of a stapled bicyclic and a linear membrane disruptive amphiphilic antimicrobial peptide (AMP) containing seven l- and four d-residues, as complexes of fucosylated analogs with the bacterial lectin LecB. The mixed chirality alpha-helices are superimposable onto the homochiral alpha-helices and form under similar conditions as shown by CD spectra and MD simulations but non-hemolytic and resistant to proteolysis. The observation of a mixed chirality alpha-helix with only natural residues in the protein environment of LecB suggests a vast unexplored territory of alpha-helical mixed chirality sequences and their possible use for optimizing bioactive alpha-helical peptides.
-
-	A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.,Baeriswyl S, Personne H, Di Bonaventura I, Kohler T, van Delden C, Stocker A, Javor S, Reymond JL RSC Chem Biol. 2021 Aug 20;2(6):1608-1617. doi: 10.1039/d1cb00124h. eCollection, 2021 Dec 2. PMID:34977576<ref>PMID:34977576</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6y0v" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:03, 1 February 2023

OCA — Wed, 01 Feb 2023 12:03:39 GMT

←Older revision		Revision as of 12:03, 1 February 2023
Line 1:		Line 1:

-	====	+	==Fucosylated bicyclic peptide bp71 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.7 Angstrom resolution==
-	<StructureSection load='6y0v' size='340' side='right'caption='[[6y0v]]' scene=''>	+	<StructureSection load='6y0v' size='340' side='right'caption='[[6y0v]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y0v]] 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=6Y0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y0V FirstGlance]. <br>
-	</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=6y0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0v OCA], [https://pdbe.org/6y0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y0v RCSB], [https://www.ebi.ac.uk/pdbsum/6y0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0v ProSAT]</span></td></tr>	+	</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=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=O65:3,5-bis(hydroxymethyl)-4-methyl-benzaldehyde'>O65</scene>, <scene name='pdbligand=ZDC:3,7-ANHYDRO-2,8-DIDEOXY-L-GLYCERO-D-GLUCO-OCTONIC+ACID'>ZDC</scene></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=6y0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0v OCA], [https://pdbe.org/6y0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y0v RCSB], [https://www.ebi.ac.uk/pdbsum/6y0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0v ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9HYN5_PSEAE Q9HYN5_PSEAE]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The peptide alpha-helix is right-handed when containing amino acids with l-chirality, and left-handed with d-chirality, however mixed chirality peptides generally do not form alpha-helices unless a helix inducer such as the non-natural residue amino-isobutyric acid is used. Herein we report the first X-ray crystal structures of mixed chirality alpha-helices in short peptides comprising only natural residues as the example of a stapled bicyclic and a linear membrane disruptive amphiphilic antimicrobial peptide (AMP) containing seven l- and four d-residues, as complexes of fucosylated analogs with the bacterial lectin LecB. The mixed chirality alpha-helices are superimposable onto the homochiral alpha-helices and form under similar conditions as shown by CD spectra and MD simulations but non-hemolytic and resistant to proteolysis. The observation of a mixed chirality alpha-helix with only natural residues in the protein environment of LecB suggests a vast unexplored territory of alpha-helical mixed chirality sequences and their possible use for optimizing bioactive alpha-helical peptides.
		+
		+	A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.,Baeriswyl S, Personne H, Di Bonaventura I, Kohler T, van Delden C, Stocker A, Javor S, Reymond JL RSC Chem Biol. 2021 Aug 20;2(6):1608-1617. doi: 10.1039/d1cb00124h. eCollection, 2021 Dec 2. PMID:34977576<ref>PMID:34977576</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y0v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Z-~~disk~~]]	+	[[Category: Pseudomonas aeruginosa]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Baeriswyl S]]
		+	[[Category: Reymond J-L]]
		+	[[Category: Stocker A]]

OCA at 06:38, 24 February 2021

OCA — Wed, 24 Feb 2021 06:38:59 GMT

←Older revision		Revision as of 06:38, 24 February 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6y0v ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6y0v' size='340' side='right'caption='[[6y0v]]' scene=''>
-	~~Authors~~: ~~Baeriswyl, S~~.~~, Stocker, A~~.~~, Reymond, J~~.-L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description: Fucosylated bicyclic peptide bp102 bound to~~ the ~~fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1~~.~~7 Angstrom resolution~~	+	</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=6y0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0v OCA], [https://pdbe.org/6y0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y0v RCSB], [https://www.ebi.ac.uk/pdbsum/6y0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0v ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Reymond~~, J.-L]]	+	__TOC__
-	[[Category: ~~Baeriswyl, S~~]]	+	</StructureSection>
-	[[Category: ~~Stocker, A~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:42, 4 March 2020

OCA — Wed, 04 Mar 2020 05:42:07 GMT

←Older revision		Revision as of 05:42, 4 March 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y0v is ON HOLD	+	The entry 6y0v is ON HOLD until Paper Publication

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

OCA: Protected "6y0v" [edit=sysop:move=sysop]

OCA — Wed, 19 Feb 2020 05:25:59 GMT

Protected "6y0v" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:25, 19 February 2020

OCA: New page: '''Unreleased structure''' The entry 6y0v is ON HOLD Authors: Baeriswyl, S., Stocker, A., Reymond, J.-L. Description: Fucosylated bicyclic peptide bp102 bound to the fucose binding lec...

OCA — Wed, 19 Feb 2020 05:25:58 GMT

New page: '''Unreleased structure''' The entry 6y0v is ON HOLD Authors: Baeriswyl, S., Stocker, A., Reymond, J.-L. Description: Fucosylated bicyclic peptide bp102 bound to the fucose binding lec...

New page

'''Unreleased structure'''

The entry 6y0v is ON HOLD

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

Description: Fucosylated bicyclic peptide bp102 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.7 Angstrom resolution
[[Category: Unreleased Structures]]
[[Category: Reymond, J.-L]]
[[Category: Baeriswyl, S]]
[[Category: Stocker, A]]