OCA at 17:20, 29 November 2023

2023-11-29T17:20:34Z

←Older revision		Revision as of 17:20, 29 November 2023
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-	====	+	==Crystal structure of Fab fragment of bevacizumab bound to DNA aptamer==
-	<StructureSection load='7v5n' size='340' side='right'caption='[[7v5n]]' scene=''>	+	<StructureSection load='7v5n' size='340' side='right'caption='[[7v5n]], [[Resolution\|resolution]] 1.70Å' 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'>[[7v5n]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=7V5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V5N 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=7v5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v5n OCA], [https://pdbe.org/7v5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v5n RCSB], [https://www.ebi.ac.uk/pdbsum/7v5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v5n ProSAT]</span></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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7v5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v5n OCA], [https://pdbe.org/7v5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v5n RCSB], [https://www.ebi.ac.uk/pdbsum/7v5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v5n ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Therapeutic monoclonal antibodies (mAbs) are successful biomedicines; however, evaluation of their pharmacokinetics and pharmacodynamics demands highly specific discrimination from human immunoglobulin G naturally present in the blood. Here, we developed a novel anti-idiotype aptamer (termed A14#1) with extraordinary specificity against the anti-vascular endothelial growth factor therapeutic mAb, bevacizumab. Structural analysis of the antibody-aptamer complex showed that several bases of A14#1 recognized only the complementarity determining region (CDR) of bevacizumab, thereby contributing to its extraordinary specificity. As the CDR of bevacizumab is predicted to be highly positively charged under mildly acidic conditions and that DNA is negatively charged, the affinity of A14#1 to bevacizumab markedly increased at pH 4.7 (K(D) = 44 pM) than at pH 7.4 (K(D) = 12 nM). A14#1-based electrochemical detection method capable of detecting 31 pM of bevacizumab at pH 4.7 was thus developed. A14#1 could be potentially useful for therapeutic drug measurement as a novel ligand of bevacizumab.
		+
		+	Development of a DNA aptamer that binds to the complementarity-determining region of therapeutic monoclonal antibody and affinity improvement induced by pH-change for sensitive detection.,Saito T, Shimizu Y, Tsukakoshi K, Abe K, Lee J, Ueno K, Asano R, Jones BV, Yamada T, Nakano T, Tong J, Hishiki A, Hara K, Hashimoto H, Sode K, Toyo'oka T, Todoroki K, Ikebukuro K Biosens Bioelectron. 2022 May 1;203:114027. doi: 10.1016/j.bios.2022.114027. Epub , 2022 Jan 22. PMID:35114463<ref>PMID:35114463</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7v5n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: Hashimoto H]]
		+	[[Category: Hishiki A]]
		+	[[Category: Todoroki K]]
		+	[[Category: Tong J]]

OCA at 07:04, 2 February 2022

2022-02-02T07:04:40Z

←Older revision		Revision as of 07:04, 2 February 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7v5n ~~is ON HOLD until Aug 17 2023~~	+	====
-		+	<StructureSection load='7v5n' size='340' side='right'caption='[[7v5n]]' scene=''>
-	~~Authors~~:	+	== 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~~:	+	</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=7v5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v5n OCA], [https://pdbe.org/7v5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v5n RCSB], [https://www.ebi.ac.uk/pdbsum/7v5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v5n ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 12:14, 29 December 2021

2021-12-29T12:14:46Z

←Older revision		Revision as of 12:14, 29 December 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7v5n is ON HOLD	+	The entry 7v5n is ON HOLD until Aug 17 2023

	Authors:		Authors:

OCA: Protected "7v5n" [edit=sysop:move=sysop]

2021-08-25T05:24:48Z

Protected "7v5n" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:24, 25 August 2021

OCA: New page: '''Unreleased structure''' The entry 7v5n is ON HOLD Authors: Description: Category: Unreleased Structures

2021-08-25T05:24:48Z

New page: '''Unreleased structure''' The entry 7v5n is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7v5n is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7v5n - Revision history

OCA at 17:20, 29 November 2023

OCA at 07:04, 2 February 2022

OCA at 12:14, 29 December 2021

OCA: Protected "7v5n" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7v5n is ON HOLD Authors: Description: Category: Unreleased Structures