3qxw - Revision history

OCA at 05:40, 15 June 2022

OCA — Wed, 15 Jun 2022 05:40:49 GMT

←Older revision		Revision as of 05:40, 15 June 2022
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	<StructureSection load='3qxw' size='340' side='right'caption='[[3qxw]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3qxw' size='340' side='right'caption='[[3qxw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxw]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QXW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxw]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i3u\|1i3u]], [[2x6m\|2x6m]], [[3qxt\|3qxt]], [[3qxv\|3qxv]], [[3qxu\|3qxu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1i3u\|1i3u]], [[2x6m\|2x6m]], [[3qxt\|3qxt]], [[3qxv\|3qxv]], [[3qxu\|3qxu]]</div></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=3qxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxw OCA], [~~http~~://pdbe.org/3qxw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qxw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qxw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxw 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=3qxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxw OCA], [https://pdbe.org/3qxw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxw RCSB], [https://www.ebi.ac.uk/pdbsum/3qxw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxw ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:52, 25 December 2019

OCA — Wed, 25 Dec 2019 09:52:54 GMT

←Older revision		Revision as of 09:52, 25 December 2019
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	==Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody==		==Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody==
-	<StructureSection load='3qxw' size='340' side='right' caption='[[3qxw]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='3qxw' size='340' side='right'caption='[[3qxw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3qxw]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXW FirstGlance]. <br>		<table><tr><td colspan='2'>[[3qxw]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXW FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Camelus glama]]		[[Category: Camelus glama]]
		+	[[Category: Large Structures]]
	[[Category: Fanning, S W]]		[[Category: Fanning, S W]]
	[[Category: Horn, J R]]		[[Category: Horn, J R]]

OCA at 10:37, 13 February 2019

OCA — Wed, 13 Feb 2019 10:37:49 GMT

←Older revision		Revision as of 10:37, 13 February 2019
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	</div>		</div>
	<div class="pdbe-citations 3qxw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3qxw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:49, 4 August 2016

OCA — Thu, 04 Aug 2016 12:49:57 GMT

←Older revision		Revision as of 12:49, 4 August 2016
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		+
	==Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody==		==Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody==
	<StructureSection load='3qxw' size='340' side='right' caption='[[3qxw]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3qxw' size='340' side='right' caption='[[3qxw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxw]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Lama_glama Lama~~ glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxw]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i3u\|1i3u]], [[2x6m\|2x6m]], [[3qxt\|3qxt]], [[3qxv\|3qxv]], [[3qxu\|3qxu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i3u\|1i3u]], [[2x6m\|2x6m]], [[3qxt\|3qxt]], [[3qxv\|3qxv]], [[3qxu\|3qxu]]</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=3qxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxw RCSB], [http://www.ebi.ac.uk/pdbsum/3qxw PDBsum]</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=3qxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxw OCA], [http://pdbe.org/3qxw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qxw RCSB], [http://www.ebi.ac.uk/pdbsum/3qxw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxw ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3qxw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lama~~ glama]]	+	[[Category: Camelus glama]]
	[[Category: Fanning, S W]]		[[Category: Fanning, S W]]
	[[Category: Horn, J R]]		[[Category: Horn, J R]]

OCA at 10:47, 19 December 2014

OCA — Fri, 19 Dec 2014 10:47:44 GMT

←Older revision		Revision as of 10:47, 19 December 2014
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-	~~{{STRUCTURE_3qxw\| PDB=3qxw \| SCENE= }}~~	+	==Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody==
-	===Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody===	+	<StructureSection load='3qxw' size='340' side='right' caption='[[3qxw]], [[Resolution\|resolution]] 1.85Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21557375}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3qxw]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i3u\|1i3u]], [[2x6m\|2x6m]], [[3qxt\|3qxt]], [[3qxv\|3qxv]], [[3qxu\|3qxu]]</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=3qxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxw RCSB], [http://www.ebi.ac.uk/pdbsum/3qxw PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Conventional anti-hapten antibodies typically bind low-molecular weight compounds (haptens) in the crevice between the variable heavy and light chains. Conversely, heavy chain-only camelid antibodies, which lack a light chain, must rely entirely on a single variable domain to recognize haptens. While several anti-hapten VHHs have been generated, little is known regarding the underlying structural and thermodynamic basis for hapten recognition. Here, an anti-methotrexate VHH (anti-MTX VHH) was generated using grafting methods whereby the three complementarity determining regions (CDRs) were inserted onto an existing VHH framework. Thermodynamic analysis of the anti-MTX VHH CDR1-3 Graft revealed a micromolar binding affinity, while the crystal structure of the complex revealed a somewhat surprising noncanonical binding site which involved MTX tunneling under the CDR1 loop. Due to the close proximity of MTX to CDR4, a nonhypervariable loop, the CDR4 loop sequence was subsequently introduced into the CDR1-3 graft, which resulted in a dramatic 1000-fold increase in the binding affinity. Crystal structure analysis of both the free and complex anti-MTX CDR1-4 graft revealed CDR4 plays a significant role in both intermolecular contacts and binding site conformation that appear to contribute toward high affinity binding. Additionally, the anti-MTX VHH possessed relatively high specificity for MTX over closely related compounds aminopterin and folate, demonstrating that VHH domains are capable of binding low-molecular weight ligands with high affinity and specificity, despite their reduced interface.

-	~~==About this Structure==~~	+	An anti-hapten camelid antibody reveals a cryptic binding site with significant energetic contributions from a nonhypervariable loop.,Fanning SW, Horn JR Protein Sci. 2011 Jul;20(7):1196-207. doi: 10.1002/pro.648. Epub 2011 May, 23. PMID:21557375<ref>PMID:21557375</ref>
-	~~[[3qxw]] is~~ a ~~5 chain structure~~ with ~~sequence~~ from ~~[http://en~~.~~wikipedia~~.~~org/wiki/Lama_glama Lama glama]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3QXW OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:021557375</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Lama glama]]		[[Category: Lama glama]]
-	[[Category: Fanning, S W.]]	+	[[Category: Fanning, S W]]
-	[[Category: Horn, J R.]]	+	[[Category: Horn, J R]]
	[[Category: Anti-hapten antibody]]		[[Category: Anti-hapten antibody]]
	[[Category: Antibody]]		[[Category: Antibody]]

OCA at 04:12, 12 September 2013

OCA — Thu, 12 Sep 2013 04:12:14 GMT

←Older revision		Revision as of 04:12, 12 September 2013
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-	[[Image:3qxw.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3qxw", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3qxw\| PDB=3qxw \| SCENE= }}		{{STRUCTURE_3qxw\| PDB=3qxw \| SCENE= }}
-
	===Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody===		===Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21557375}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21557375 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21557375}}		{{ABSTRACT_PUBMED_21557375}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:021557375</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021557375</ref><references group="xtra"/><references/>
	[[Category: Lama glama]]		[[Category: Lama glama]]
	[[Category: Fanning, S W.]]		[[Category: Fanning, S W.]]

OCA at 06:06, 27 July 2011

OCA — Wed, 27 Jul 2011 06:06:45 GMT

←Older revision		Revision as of 06:06, 27 July 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3qxw.jpg\|left\|200px]]

-	The ~~entry 3qxw~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3qxw", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3qxw\| PDB=3qxw \| SCENE= }}

-	~~Authors: Fanning, S.W., Horn, J.R.~~	+	===Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody===

-	~~Description~~: ~~Free~~ structure ~~of an anti~~-~~methotrexate CDR1~~-~~4 Graft VHH~~ Antibody	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21557375}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21557375 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21557375}}
		+
		+	==About this Structure==
		+	[[3qxw]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXW OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021557375</ref><references group="xtra"/>
		+	[[Category: Lama glama]]
		+	[[Category: Fanning, S W.]]
		+	[[Category: Horn, J R.]]
		+	[[Category: Anti-hapten antibody]]
		+	[[Category: Antibody]]
		+	[[Category: Camelid single domain antibody]]
		+	[[Category: Cdr]]
		+	[[Category: Hapten binding]]
		+	[[Category: Heavy chain only]]
		+	[[Category: Immune system]]
		+	[[Category: Ligand binding]]
		+	[[Category: Low molecular weight compound]]
		+	[[Category: Methotrexate]]
		+	[[Category: Small molecule sensing]]
		+	[[Category: Vhh]]

OCA at 04:18, 12 May 2011

OCA — Thu, 12 May 2011 04:18:34 GMT

←Older revision		Revision as of 04:18, 12 May 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3qxw is ON HOLD	+	The entry 3qxw is ON HOLD until Paper Publication

	Authors: Fanning, S.W., Horn, J.R.		Authors: Fanning, S.W., Horn, J.R.

	Description: Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody		Description: Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody

OCA at 06:47, 23 March 2011

OCA — Wed, 23 Mar 2011 06:47:32 GMT

←Older revision		Revision as of 06:47, 23 March 2011
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	Authors: Fanning, S.W., Horn, J.R.		Authors: Fanning, S.W., Horn, J.R.

-	Description: Free ~~Structure~~ of an ~~Anti~~-~~Methotrexate~~ CDR1-4 Graft VHH Antibody	+	Description: Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody

OCA: Protected "3qxw" [edit=sysop:move=sysop]

OCA — Wed, 09 Mar 2011 06:10:36 GMT

Protected "3qxw" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:10, 9 March 2011