5bjz - Revision history

OCA at 08:27, 27 September 2023

2023-09-27T08:27:14Z

←Older revision		Revision as of 08:27, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bjz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7] 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=5BJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BJZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bjz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7] 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=5BJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BJZ 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</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]] 1.95Å</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</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=5bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bjz OCA], [https://pdbe.org/5bjz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bjz RCSB], [https://www.ebi.ac.uk/pdbsum/5bjz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bjz 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=5bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bjz OCA], [https://pdbe.org/5bjz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bjz RCSB], [https://www.ebi.ac.uk/pdbsum/5bjz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bjz ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:42, 31 May 2023

2023-05-31T06:42:19Z

←Older revision		Revision as of 06:42, 31 May 2023
Line 1:		Line 1:

	==Crystal structure of maltose binding protein in complex with an allosteric synthetic antibody==		==Crystal structure of maltose binding protein in complex with an allosteric synthetic antibody==
-	<StructureSection load='5bjz' size='340' side='right' caption='[[5bjz]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5bjz' size='340' side='right'caption='[[5bjz]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bjz]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Eco57 Eco57~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BJZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bjz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7] 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=5BJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BJZ 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=~~GOL~~:~~GLYCEROL~~'>~~GOL~~</scene>, <scene name='pdbligand=~~MAL~~:~~MALTOSE~~'>~~MAL~~</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">malE, Z5632, ECs5017 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])~~</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=5bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bjz OCA], [https://pdbe.org/5bjz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bjz RCSB], [https://www.ebi.ac.uk/pdbsum/5bjz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bjz 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=5bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bjz OCA], [~~http~~://pdbe.org/5bjz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5bjz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5bjz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5bjz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~MALE_ECO57 MALE_ECO57]~~] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides ~~(By similarity)~~.	+	[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 ==
Line 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5bjz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5bjz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 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: ~~Eco57]]~~	+	[[Category: Escherichia coli O157:H7]]
-	~~[[Category~~: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Kossiakoff, A A~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Mukherjee, S~~]]	+	[[Category: Kossiakoff AA]]
-	[[Category: ~~Conformation specific synthetic antibody~~]]	+	[[Category: Mukherjee S]]
-	[[Category: ~~Maltose binding protein]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 20:27, 24 January 2018

2018-01-24T20:27:34Z

←Older revision		Revision as of 20:27, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5bjz' size='340' side='right' caption='[[5bjz]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5bjz' size='340' side='right' caption='[[5bjz]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bjz]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bjz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco57 Eco57] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BJZ 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAL:MALTOSE'>MAL</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAL:MALTOSE'>MAL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">malE, Z5632, ECs5017 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</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=5bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bjz OCA], [http://pdbe.org/5bjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bjz RCSB], [http://www.ebi.ac.uk/pdbsum/5bjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bjz 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=5bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bjz OCA], [http://pdbe.org/5bjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bjz RCSB], [http://www.ebi.ac.uk/pdbsum/5bjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bjz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/MALE_ECO57 MALE_ECO57]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides (By similarity).		[[http://www.uniprot.org/uniprot/MALE_ECO57 MALE_ECO57]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides (By similarity).
		+	<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 5bjz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Eco57]]
		+	[[Category: Human]]
	[[Category: Kossiakoff, A A]]		[[Category: Kossiakoff, A A]]
	[[Category: Mukherjee, S]]		[[Category: Mukherjee, S]]

OCA at 06:44, 17 January 2018

2018-01-17T06:44:47Z

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

-	~~The entry~~ 5bjz is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of maltose binding protein in complex with an allosteric synthetic antibody==
-		+	<StructureSection load='5bjz' size='340' side='right' caption='[[5bjz]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5bjz]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BJZ 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAL:MALTOSE'>MAL</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=5bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bjz OCA], [http://pdbe.org/5bjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bjz RCSB], [http://www.ebi.ac.uk/pdbsum/5bjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bjz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MALE_ECO57 MALE_ECO57]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides (By similarity).
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kossiakoff, A A]]
		+	[[Category: Mukherjee, S]]
		+	[[Category: Conformation specific synthetic antibody]]
		+	[[Category: Maltose binding protein]]
		+	[[Category: Sugar binding protein]]

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

2017-09-27T10:37:00Z

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

←Older revision

Revision as of 10:37, 27 September 2017

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

2017-09-27T10:36:59Z

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

New page

'''Unreleased structure'''

The entry 5bjz is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]