5bk1 - Revision history

OCA at 08:27, 27 September 2023

OCA — Wed, 27 Sep 2023 08:27:15 GMT

←Older revision		Revision as of 08:27, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bk1]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BK1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bk1]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BK1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.15Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5bk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bk1 OCA], [https://pdbe.org/5bk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bk1 RCSB], [https://www.ebi.ac.uk/pdbsum/5bk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bk1 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=5bk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bk1 OCA], [https://pdbe.org/5bk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bk1 RCSB], [https://www.ebi.ac.uk/pdbsum/5bk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bk1 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:42, 31 May 2023

OCA — Wed, 31 May 2023 06:42:24 GMT

←Older revision		Revision as of 06:42, 31 May 2023
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	<StructureSection load='5bk1' size='340' side='right'caption='[[5bk1]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5bk1' size='340' side='right'caption='[[5bk1]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bk1]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BK1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bk1]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BK1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5bk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bk1 OCA], [~~http~~://pdbe.org/5bk1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5bk1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5bk1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5bk1 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=5bk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bk1 OCA], [https://pdbe.org/5bk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bk1 RCSB], [https://www.ebi.ac.uk/pdbsum/5bk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bk1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[Maltose-binding protein 3D structures\|Maltose-binding protein 3D structures]]		*[[Maltose-binding protein 3D structures\|Maltose-binding protein 3D structures]]
		+	*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kossiakoff~~, A A~~]]	+	[[Category: Kossiakoff AA]]
-	[[Category: Mukherjee, S]]	+	[[Category: Mukherjee S]]
-	~~[[Category: Conformation specific synthetic antibody]]~~	+
-	~~[[Category: Maltose binding protein]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 08:49, 11 March 2020

OCA — Wed, 11 Mar 2020 08:49:22 GMT

←Older revision		Revision as of 08:49, 11 March 2020
Line 1:		Line 1:

	==Crystal structure of maltose binding protein in complex with an endosteric synthetic antibody==		==Crystal structure of maltose binding protein in complex with an endosteric synthetic antibody==
-	<StructureSection load='5bk1' size='340' side='right' caption='[[5bk1]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='5bk1' size='340' side='right'caption='[[5bk1]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bk1]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BK1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bk1]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BK1 FirstGlance]. <br>
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 5bk1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5bk1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Maltose-binding protein 3D structures\|Maltose-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 26:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Kossiakoff, A A]]		[[Category: Kossiakoff, A A]]
	[[Category: Mukherjee, S]]		[[Category: Mukherjee, S]]

OCA at 20:27, 24 January 2018

OCA — Wed, 24 Jan 2018 20:27:41 GMT

←Older revision		Revision as of 20:27, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5bk1' size='340' side='right' caption='[[5bk1]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5bk1' size='340' side='right' caption='[[5bk1]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bk1]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bk1]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BK1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5bk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bk1 OCA], [http://pdbe.org/5bk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bk1 RCSB], [http://www.ebi.ac.uk/pdbsum/5bk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bk1 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=5bk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bk1 OCA], [http://pdbe.org/5bk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bk1 RCSB], [http://www.ebi.ac.uk/pdbsum/5bk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bk1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Conformational changes in proteins due to ligand binding are ubiquitous in biological systems and are integral to many biological systems. However, it is often challenging to link ligand-induced conformational changes to a resulting biological function because it is difficult to distinguish between the energetic components associated with ligand-binding and those due to structural rearrangements. Here, we used a unique approach exploiting conformation-specific and regio-specific synthetic antibodies (sABs) to probe the energetic contributions of ligand-binding to conformation changes. Using maltose binding protein (MBP) as a model system, customized phage display selections were performed to generate sABs that stabilize MBP in different conformational states, modulating ligand binding affinity in competitive, allosteric or peristeric manners. We determined that the binding of a closed conformation-specific sAB (sAB-11M) to MBP in the absence of maltose is entropically driven, providing new insight into designing antibody stabilized protein interactions. Crystal structures of sABs bound to MBP, together with biophysical data delineate the basis of free energy differences between different conformational states and confirm the use of the sABs as energy probes for dissecting enthalpic and entropic contributions to conformational transitions. Our work provides a foundation for investigating the energetic contributions of distinct conformational dynamics to specific biological outputs. We anticipate that our approach also may be valuable for analyzing the energy landscapes of regulatory proteins controlling biological responses to environmental changes.
		+
		+	Engineered synthetic antibodies as probes to quantify the energetic contributions of ligand binding to conformational changes in proteins.,Mukherjee S, Griffin DH, Horn JR, Rizk SS, Nocula-Lugowska M, Malmqvist M, Kim SS, Kossiakoff AA J Biol Chem. 2018 Jan 10. pii: RA117.000656. doi: 10.1074/jbc.RA117.000656. PMID:29321208<ref>PMID:29321208</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5bk1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Human]]
	[[Category: Kossiakoff, A A]]		[[Category: Kossiakoff, A A]]
	[[Category: Mukherjee, S]]		[[Category: Mukherjee, S]]

OCA at 06:44, 17 January 2018

OCA — Wed, 17 Jan 2018 06:44:46 GMT

←Older revision		Revision as of 06:44, 17 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5bk1 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of maltose binding protein in complex with an endosteric synthetic antibody==
-		+	<StructureSection load='5bk1' size='340' side='right' caption='[[5bk1]], [[Resolution\|resolution]] 2.15Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5bk1]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BK1 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5bk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bk1 OCA], [http://pdbe.org/5bk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bk1 RCSB], [http://www.ebi.ac.uk/pdbsum/5bk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bk1 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kossiakoff, A A]]
		+	[[Category: Mukherjee, S]]
		+	[[Category: Conformation specific synthetic antibody]]
		+	[[Category: Maltose binding protein]]
		+	[[Category: Sugar binding protein]]

OCA at 06:20, 22 November 2017

OCA — Wed, 22 Nov 2017 06:20:52 GMT

←Older revision		Revision as of 06:20, 22 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5bk1 is ON HOLD	+	The entry 5bk1 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5bk1" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 10:37:19 GMT

Protected "5bk1" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:37, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5bk1 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 10:37:18 GMT

New page: '''Unreleased structure''' The entry 5bk1 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5bk1 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]