5mfo - Revision history

OCA at 18:42, 1 November 2023

OCA — Wed, 01 Nov 2023 18:42:19 GMT

←Older revision		Revision as of 18:42, 1 November 2023
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	<StructureSection load='5mfo' size='340' side='right'caption='[[5mfo]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='5mfo' size='340' side='right'caption='[[5mfo]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mfo]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MFO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5MFO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mfo]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MFO 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=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.3Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5mfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mfo OCA], [~~http~~://pdbe.org/5mfo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mfo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mfo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mfo ProSAT]</span></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=EDO:1,2-ETHANEDIOL'>EDO</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=5mfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mfo OCA], [https://pdbe.org/5mfo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mfo RCSB], [https://www.ebi.ac.uk/pdbsum/5mfo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mfo ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5mfo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5mfo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 21:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Ernst, P]]	+	[[Category: Ernst P]]
-	[[Category: Ewald, C]]	+	[[Category: Ewald C]]
-	[[Category: Hansen, S]]	+	[[Category: Hansen S]]
-	[[Category: Mittl, P]]	+	[[Category: Mittl P]]
-	[[Category: Plueckthun, A]]	+	[[Category: Plueckthun A]]
-	[[Category: Reichen, C]]	+	[[Category: Reichen C]]
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Designed armadillo repeat protein]]~~	+
-	~~[[Category: Peptide binding~~]]	+

OCA at 07:18, 19 August 2020

OCA — Wed, 19 Aug 2020 07:18:13 GMT

←Older revision		Revision as of 07:18, 19 August 2020
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	==Designed armadillo repeat protein YIIIM3AIII==		==Designed armadillo repeat protein YIIIM3AIII==
-	<StructureSection load='5mfo' size='340' side='right' caption='[[5mfo]], [[Resolution\|resolution]] 1.30Å' scene=''>	+	<StructureSection load='5mfo' size='340' side='right'caption='[[5mfo]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mfo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MFO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MFO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mfo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MFO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MFO 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=EDO:1,2-ETHANEDIOL'>EDO</scene></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=EDO:1,2-ETHANEDIOL'>EDO</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=5mfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mfo OCA], [http://pdbe.org/5mfo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mfo RCSB], [http://www.ebi.ac.uk/pdbsum/5mfo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mfo ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5mfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mfo OCA], [http://pdbe.org/5mfo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mfo RCSB], [http://www.ebi.ac.uk/pdbsum/5mfo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mfo ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Ernst, P]]		[[Category: Ernst, P]]

OCA at 07:42, 22 February 2018

OCA — Thu, 22 Feb 2018 07:42:51 GMT

←Older revision		Revision as of 07:42, 22 February 2018
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	<StructureSection load='5mfo' size='340' side='right' caption='[[5mfo]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='5mfo' size='340' side='right' caption='[[5mfo]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mfo]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MFO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mfo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MFO 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=EDO:1,2-ETHANEDIOL'>EDO</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=EDO:1,2-ETHANEDIOL'>EDO</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=5mfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mfo OCA], [http://pdbe.org/5mfo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mfo RCSB], [http://www.ebi.ac.uk/pdbsum/5mfo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mfo 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=5mfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mfo OCA], [http://pdbe.org/5mfo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mfo RCSB], [http://www.ebi.ac.uk/pdbsum/5mfo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mfo ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Synthetic construct sequences]]
	[[Category: Ernst, P]]		[[Category: Ernst, P]]
	[[Category: Ewald, C]]		[[Category: Ewald, C]]

OCA at 10:28, 13 September 2017

OCA — Wed, 13 Sep 2017 10:28:58 GMT

←Older revision		Revision as of 10:28, 13 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5mfo is ~~ON HOLD until Paper~~ Publication	+	==Designed armadillo repeat protein YIIIM3AIII==
		+	<StructureSection load='5mfo' size='340' side='right' caption='[[5mfo]], [[Resolution\|resolution]] 1.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5mfo]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MFO 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=EDO:1,2-ETHANEDIOL'>EDO</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=5mfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mfo OCA], [http://pdbe.org/5mfo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mfo RCSB], [http://www.ebi.ac.uk/pdbsum/5mfo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mfo ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Designed armadillo repeat proteins (dArmRP) were developed to create a modular peptide binding technology where each of the structural repeats binds two residues of the target peptide. An essential prerequisite for such a technology is a dArmRP geometry that matches the peptide bond length. To this end, we determined a large set (n=27) of dArmRP X-ray structures, of which 14 were previously unpublished, to calculate curvature parameters that define their geometry. Our analysis shows that consensus dArmRPs exhibit curvatures close to the optimal range for modular peptide recognition. Binding of peptide ligands can induce a curvature within the desired range, as confirmed by single-molecule FRET experiments in solution. On the other hand, computationally designed ArmRPs, where side chains have been chosen with the intention to optimally fit into a geometrically optimized backbone, turned out to be more divergent in reality, and thus not suitable for continuous peptide binding. Furthermore, we show that the formation of a crystal lattice can induce small but significant deviations from the curvature adopted in solution, which can interfere with the evaluation of repeat protein scaffolds when high accuracy is required. This study corroborates the suitability of consensus dArmRP as a scaffold for the development of modular peptide binders.

-	~~Authors~~:	+	Curvature of designed armadillo repeat proteins allows modular peptide binding.,Hansen S, Ernst P, Konig SLB, Reichen C, Ewald C, Nettels D, Mittl PRE, Schuler B, Pluckthun A J Struct Biol. 2017 Aug 29. pii: S1047-8477(17)30140-5. doi:, 10.1016/j.jsb.2017.08.009. PMID:28864298<ref>PMID:28864298</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5mfo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ernst, P]]
		+	[[Category: Ewald, C]]
		+	[[Category: Hansen, S]]
		+	[[Category: Mittl, P]]
		+	[[Category: Plueckthun, A]]
		+	[[Category: Reichen, C]]
		+	[[Category: De novo protein]]
		+	[[Category: Designed armadillo repeat protein]]
		+	[[Category: Peptide binding]]

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

OCA — Fri, 09 Dec 2016 16:46:59 GMT

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

←Older revision

Revision as of 16:46, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5mfo is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Dec 2016 16:46:58 GMT

New page: '''Unreleased structure''' The entry 5mfo is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5mfo is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]