5ien - Revision history

OCA at 13:48, 30 August 2023

OCA — Wed, 30 Aug 2023 13:48:41 GMT

←Older revision		Revision as of 13:48, 30 August 2023
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	<StructureSection load='5ien' size='340' side='right'caption='[[5ien]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='5ien' size='340' side='right'caption='[[5ien]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ien]] is a 2 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=5IEN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IEN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ien]] is a 2 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=5IEN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IEN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VDY:3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL'>VDY</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]] 2.089Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ieo\|5ieo]], [[5iep\|5iep]], [[5ier\|5ier]], [[5if6\|5if6]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VDY:3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL'>VDY</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=5ien FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ien OCA], [~~http~~://pdbe.org/5ien PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ien RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ien PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ien 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=5ien FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ien OCA], [https://pdbe.org/5ien PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ien RCSB], [https://www.ebi.ac.uk/pdbsum/5ien PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ien ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Doyle~~, L A~~]]	+	[[Category: Doyle LA]]
-	[[Category: Stoddard~~, B L]]~~	+	[[Category: Stoddard BL]]
-	~~[[Category: Computational]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Ligand binder]]~~	+
-	~~[[Category: Rossetta]]~~	+
-	~~[[Category: Structural genomic~~]]	+

OCA at 04:33, 13 February 2020

OCA — Thu, 13 Feb 2020 04:33:38 GMT

←Older revision		Revision as of 04:33, 13 February 2020
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	<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=5ien FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ien OCA], [http://pdbe.org/5ien PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ien RCSB], [http://www.ebi.ac.uk/pdbsum/5ien PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ien 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=5ien FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ien OCA], [http://pdbe.org/5ien PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ien RCSB], [http://www.ebi.ac.uk/pdbsum/5ien PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ien ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Attempts to create novel ligand-binding proteins often focus on formation of a binding pocket with shape complementarity against the desired ligand (particularly for compounds that lack distinct polar moieties). Although designed proteins often exhibit binding of the desired ligand, in some cases they display unintended recognition behavior. One such designed protein, that was originally intended to bind tetrahydrocannabinol (THC), was found instead to display binding of 25-hydroxy-cholecalciferol (25-D3) and was subjected to biochemical characterization, further selections for enhanced 25-D3 binding affinity and crystallographic analyses. The deviation in specificity is due in part to unexpected altertion of its conformation, corresponding to a significant change of the orientation of an alpha-helix and an equally large movement of a loop, both of which flank the designed ligand-binding pocket. Those changes led to engineered protein constructs that exhibit significantly more contacts and complementarity towards the 25-D3 ligand than the initial designed protein had been predicted to form towards its intended THC ligand. Molecular dynamics simulations imply that the initial computationally designed mutations may contribute to the movement of the helix. These analyses collectively indicate that accurate prediction and control of backbone dynamics conformation, through a combination of improved conformational sampling and/or de novo structure design, represents a key area of further development for the design and optimization of engineered ligand-binding proteins.
		+
		+	Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold.,Day AL, Greisen P, Doyle L, Schena A, Stella N, Johnsson K, Baker D, Stoddard B Protein Eng Des Sel. 2018 Oct 1;31(10):375-387. doi: 10.1093/protein/gzy031. PMID:30566669<ref>PMID:30566669</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ien" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:48, 25 December 2019

OCA — Wed, 25 Dec 2019 11:48:00 GMT

←Older revision		Revision as of 11:48, 25 December 2019
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	==Structure of CDL2.2, a computationally designed Vitamin-D3 binder==		==Structure of CDL2.2, a computationally designed Vitamin-D3 binder==
-	<StructureSection load='5ien' size='340' side='right' caption='[[5ien]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='5ien' size='340' side='right'caption='[[5ien]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ien]] is a 2 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=5IEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IEN FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ien]] is a 2 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=5IEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IEN FirstGlance]. <br>
Line 10:		Line 10:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Doyle, L A]]		[[Category: Doyle, L A]]

OCA at 08:46, 18 July 2018

OCA — Wed, 18 Jul 2018 08:46:05 GMT

←Older revision		Revision as of 08:46, 18 July 2018
Line 1:		Line 1:

-	==Structure of ~~D30H_F14~~, a computationally designed Vitamin-D3 binder==	+	==Structure of CDL2.2, a computationally designed Vitamin-D3 binder==
	<StructureSection load='5ien' size='340' side='right' caption='[[5ien]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='5ien' size='340' side='right' caption='[[5ien]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 12:50, 6 November 2017

OCA — Mon, 06 Nov 2017 12:50:41 GMT

←Older revision		Revision as of 12:50, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5ien' size='340' side='right' caption='[[5ien]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='5ien' size='340' side='right' caption='[[5ien]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ien]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IEN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ien]] is a 2 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=5IEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IEN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VDY:3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL'>VDY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VDY:3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL'>VDY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ieo\|5ieo]], [[5iep\|5iep]], [[5ier\|5ier]], [[5if6\|5if6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ieo\|5ieo]], [[5iep\|5iep]], [[5ier\|5ier]], [[5if6\|5if6]]</td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Synthetic construct sequences]]
	[[Category: Doyle, L A]]		[[Category: Doyle, L A]]
	[[Category: Stoddard, B L]]		[[Category: Stoddard, B L]]

OCA at 09:33, 11 March 2017

OCA — Sat, 11 Mar 2017 09:33:15 GMT

←Older revision		Revision as of 09:33, 11 March 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5ien is ~~ON HOLD until Paper Publication~~	+	==Structure of D30H_F14, a computationally designed Vitamin-D3 binder==
-		+	<StructureSection load='5ien' size='340' side='right' caption='[[5ien]], [[Resolution\|resolution]] 2.09Å' scene=''>
-	~~Authors~~: ~~Stoddard~~, B.L., ~~Doyle~~, L.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ien]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IEN FirstGlance]. <br>
-	~~Description~~: ~~Structure of D30H_F14~~, ~~a computationally designed Vitamin~~-~~D3 binder~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VDY:3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL'>VDY</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ieo\|5ieo]], [[5iep\|5iep]], [[5ier\|5ier]], [[5if6\|5if6]]</td></tr>
-	[[Category: Stoddard, B.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=5ien FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ien OCA], [http://pdbe.org/5ien PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ien RCSB], [http://www.ebi.ac.uk/pdbsum/5ien PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ien ProSAT]</span></td></tr>
-	[[Category: ~~Doyle, L.A~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Doyle, L A]]
		+	[[Category: Stoddard, B L]]
		+	[[Category: Computational]]
		+	[[Category: De novo protein]]
		+	[[Category: Ligand binder]]
		+	[[Category: Rossetta]]
		+	[[Category: Structural genomic]]

OCA at 19:28, 23 June 2016

OCA — Thu, 23 Jun 2016 19:28:13 GMT

←Older revision		Revision as of 19:28, 23 June 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ien is ON HOLD until ~~Sep 21 2017~~	+	The entry 5ien is ON HOLD until Paper Publication

	Authors: Stoddard, B.L., Doyle, L.A.		Authors: Stoddard, B.L., Doyle, L.A.

OCA at 11:56, 20 June 2016

OCA — Mon, 20 Jun 2016 11:56:00 GMT

←Older revision		Revision as of 11:56, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ien is ON HOLD until ~~Paper Publication~~	+	The entry 5ien is ON HOLD until Sep 21 2017

	Authors: Stoddard, B.L., Doyle, L.A.		Authors: Stoddard, B.L., Doyle, L.A.

OCA at 00:26, 11 May 2016

OCA — Wed, 11 May 2016 00:26:30 GMT

←Older revision		Revision as of 00:26, 11 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Stoddard, B.L., Doyle, L.A.		Authors: Stoddard, B.L., Doyle, L.A.

OCA at 02:12, 10 March 2016

OCA — Thu, 10 Mar 2016 02:12:01 GMT

←Older revision		Revision as of 02:12, 10 March 2016
Line 3:		Line 3:
	The entry 5ien is ON HOLD		The entry 5ien is ON HOLD

-	Authors: Stoddard, ~~Barry~~ L., Doyle, ~~Lindsey~~ A.	+	Authors: Stoddard, B.L., Doyle, L.A.

	Description: Structure of D30H_F14, a computationally designed Vitamin-D3 binder		Description: Structure of D30H_F14, a computationally designed Vitamin-D3 binder
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Stoddard, ~~Barry~~ L]]	+	[[Category: Stoddard, B.L]]
-	[[Category: Doyle, ~~Lindsey~~ A]]	+	[[Category: Doyle, L.A]]