6bjz - Revision history

OCA at 14:43, 4 October 2023

2023-10-04T14:43:53Z

←Older revision		Revision as of 14:43, 4 October 2023
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	<StructureSection load='6bjz' size='340' side='right'caption='[[6bjz]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='6bjz' size='340' side='right'caption='[[6bjz]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bjz]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6BJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bjz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BJZ FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=DV7:'>DV7</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]] 1.45Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1i9r\|1i9r]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DV7:L-(7-hydroxycoumarin-4-yl)ethylglycine'>DV7</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjz OCA], [~~http~~://pdbe.org/6bjz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bjz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bjz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjz 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=6bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjz OCA], [https://pdbe.org/6bjz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bjz RCSB], [https://www.ebi.ac.uk/pdbsum/6bjz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 6bjz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6bjz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Henderson~~, J N~~]]	+	[[Category: Henderson JN]]
-	[[Category: Mills~~, J H~~]]	+	[[Category: Mills JH]]
-	[[Category: Simmons~~, C R]]~~	+	[[Category: Simmons CR]]
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immunoglobulin]]~~	+
-	~~[[Category: Non canonical aminoacid~~]]	+

OCA at 10:45, 24 December 2020

2020-12-24T10:45:14Z

←Older revision		Revision as of 10:45, 24 December 2020
Line 3:		Line 3:
	<StructureSection load='6bjz' size='340' side='right'caption='[[6bjz]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='6bjz' size='340' side='right'caption='[[6bjz]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bjz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6BJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bjz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6BJZ FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DV7:'>DV7</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DV7:'>DV7</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i9r\|1i9r]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1i9r\|1i9r]]</div></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjz OCA], [http://pdbe.org/6bjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bjz RCSB], [http://www.ebi.ac.uk/pdbsum/6bjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjz ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjz OCA], [http://pdbe.org/6bjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bjz RCSB], [http://www.ebi.ac.uk/pdbsum/6bjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjz ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Genetically encoded fluorescent noncanonical amino acids (fNCAAs) could be used to develop novel fluorescent sensors of protein function. Previous efforts toward this goal have been limited by the lack of extensive physicochemical and structural characterizations of protein-based sensors containing fNCAAs. Here, we report the steady-state spectroscopic properties and first structural analyses of an fNCAA-containing Fab fragment of the 5c8 antibody, which binds human CD40L. A previously reported 5c8 variant in which the light chain residue Ile(L)98 is replaced with the fNCAA l-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) exhibits a 1.7-fold increase in fluorescence upon antigen binding. Determination and comparison of the apparent pKas of 7-HCAA in the unbound and bound forms indicate that the observed increase in fluorescence is not the result of perturbations in pKa. Crystal structures of the fNCAA-containing Fab in the apo and bound forms reveal interactions between the 7-HCAA side chain and surrounding residues that are disrupted upon antigen binding. This structural characterization not only provides insight into the manner in which protein environments can modulate the fluorescence properties of 7-HCAA but also could serve as a starting point for the rational design of new fluorescent protein-based reporters of protein function.
		+
		+	Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore.,Henderson JN, Simmons CR, Fahmi NE, Jeffs JW, Borges CR, Mills JH Biochemistry. 2020 Sep 22;59(37):3401-3410. doi: 10.1021/acs.biochem.0c00474., Epub 2020 Sep 3. PMID:32845612<ref>PMID:32845612</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6bjz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Henderson, J N]]		[[Category: Henderson, J N]]

OCA at 08:50, 11 November 2020

2020-11-11T08:50:27Z

←Older revision		Revision as of 08:50, 11 November 2020
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	==Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine at pH 5.5==		==Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine at pH 5.5==
-	<StructureSection load='6bjz' size='340' side='right' caption='[[6bjz]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='6bjz' size='340' side='right'caption='[[6bjz]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bjz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bjz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6BJZ FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DV7:'>DV7</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DV7:'>DV7</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i9r\|1i9r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i9r\|1i9r]]</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=6bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjz OCA], [http://pdbe.org/6bjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bjz RCSB], [http://www.ebi.ac.uk/pdbsum/6bjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjz ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjz OCA], [http://pdbe.org/6bjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bjz RCSB], [http://www.ebi.ac.uk/pdbsum/6bjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjz ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Henderson, J N]]		[[Category: Henderson, J N]]
	[[Category: Mills, J H]]		[[Category: Mills, J H]]

OCA at 08:06, 14 November 2018

2018-11-14T08:06:50Z

←Older revision		Revision as of 08:06, 14 November 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6bjz is ON HOLD until Paper Publication~~	+	==Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine at pH 5.5==
-		+	<StructureSection load='6bjz' size='340' side='right' caption='[[6bjz]], [[Resolution\|resolution]] 1.45Å' scene=''>
-	~~Authors: Henderson, J.N., Simmons, C.R., Mills, J.H.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6bjz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BJZ FirstGlance]. <br>
-	~~Description:~~ Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine at pH 5.5	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DV7:'>DV7</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i9r\|1i9r]]</td></tr>
-	[[Category: Mills, J.H]]	+	<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=6bjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjz OCA], [http://pdbe.org/6bjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bjz RCSB], [http://www.ebi.ac.uk/pdbsum/6bjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjz ProSAT]</span></td></tr>
-	[[Category: Simmons, C.R]]	+	</table>
-	[[Category: ~~Henderson, J.N~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Henderson, J N]]
		+	[[Category: Mills, J H]]
		+	[[Category: Simmons, C R]]
		+	[[Category: Immune system]]
		+	[[Category: Immunoglobulin]]
		+	[[Category: Non canonical aminoacid]]

OCA at 05:50, 13 December 2017

2017-12-13T05:50:43Z

←Older revision		Revision as of 05:50, 13 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6bjz is ON HOLD	+	The entry 6bjz is ON HOLD until Paper Publication

	Authors: Henderson, J.N., Simmons, C.R., Mills, J.H.		Authors: Henderson, J.N., Simmons, C.R., Mills, J.H.

OCA: Protected "6bjz" [edit=sysop:move=sysop]

2017-11-15T06:23:54Z

Protected "6bjz" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:23, 15 November 2017

OCA: New page: '''Unreleased structure''' The entry 6bjz is ON HOLD Authors: Henderson, J.N., Simmons, C.R., Mills, J.H. Description: Crystal Structure of the Fab fragment of humanized 5c8 antibody c...

2017-11-15T06:23:53Z

New page: '''Unreleased structure''' The entry 6bjz is ON HOLD Authors: Henderson, J.N., Simmons, C.R., Mills, J.H. Description: Crystal Structure of the Fab fragment of humanized 5c8 antibody c...

New page

'''Unreleased structure'''

The entry 6bjz is ON HOLD

Authors: Henderson, J.N., Simmons, C.R., Mills, J.H.

Description: Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine at pH 5.5
[[Category: Unreleased Structures]]
[[Category: Mills, J.H]]
[[Category: Simmons, C.R]]
[[Category: Henderson, J.N]]