1gpo - Revision history

OCA at 11:23, 27 March 2024

OCA — Wed, 27 Mar 2024 11:23:35 GMT

←Older revision		Revision as of 11:23, 27 March 2024
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	<StructureSection load='1gpo' size='340' side='right'caption='[[1gpo]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1gpo' size='340' side='right'caption='[[1gpo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GPO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=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=1gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpo OCA], [https://pdbe.org/1gpo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gpo RCSB], [https://www.ebi.ac.uk/pdbsum/1gpo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gpo 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=1gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpo OCA], [https://pdbe.org/1gpo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gpo RCSB], [https://www.ebi.ac.uk/pdbsum/1gpo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gpo ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/IGKC_MOUSE IGKC_MOUSE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gpo ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gpo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	In a protein design study the artificial antibody M41 was modelled with its binding site complementary to the protease inhibitor cystatin, which was chosen as a structurally well-characterized "antigen". The modelling of M41 took advantage of the crystal structure of the anti-lysozyme antibody HyHEL-10 as a structural template. Its combining site was reshaped by replacing 19 amino acid side-chains in the hypervariable loops. In addition, ten amino acid residues were substituted in the framework regions. The crystal structure of the corresponding antibody model M41, which was produced as an F(ab) fragment in Escherichia coli, was determined at a resolution of 1.95 A. The crystals exhibited symmetry of the space group P2(1)2(1)2(1) (a = 96.5 A; b = 103.5 A; c = 113.6 A) with two F(ab) fragments in the asymmetric unit, which were independently refined (final R-factor 21.7%). The resulting coordinates were used for a detailed comparison with the modelled protein structure. It was found that the mutual arrangement of the six complementarity-determining regions as well as most of their backbone conformation had been correctly predicted. One major difference that was detected for the conformation of a five residue insertion in complementarity-determining region L1 could be explained by an erroneously defined segment in the structure of the antibody 4-4-20, which had been used as a template for this loop. In the light of more recent crystallographic data it appears that this segment adopts a new canonical structure. Apart from this region, most of the side-chains in the antigen-binding site had been properly placed in the M41 model. There was however one important exception concerning Trp H98, whose side-chain conformation had been kept as it appeared in HyHEL-10. The differing orientation of this residue in the model compared with the crystal structure of the artificial F(ab) fragment M41 explains why an antigen affinity could not be detected so far. The detailed analysis of this and other, more subtle deviations suggests how to make this F(ab) fragment function by introducing a few additional amino acid changes into M41.
-
-	The rational construction of an antibody against cystatin: lessons from the crystal structure of an artificial Fab fragment.,Schiweck W, Skerra A J Mol Biol. 1997 May 23;268(5):934-51. PMID:9180382<ref>PMID:9180382</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1gpo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 31:		Line 25:
	*[[Sandbox 20009\|Sandbox 20009]]		*[[Sandbox 20009\|Sandbox 20009]]
	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]		*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Schiweck, W]]	+	[[Category: Schiweck W]]
-	[[Category: Skerra, A]]	+	[[Category: Skerra A]]
-	~~[[Category: Antibody design]]~~	+
-	~~[[Category: Antigen-binding site]]~~	+
-	~~[[Category: Canonical conformation]]~~	+
-	~~[[Category: Complementarity-determining region]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immunoglobulin structure]]~~	+
-	~~[[Category: Protein engineering~~]]	+

OCA at 11:27, 28 July 2021

OCA — Wed, 28 Jul 2021 11:27:04 GMT

←Older revision		Revision as of 11:27, 28 July 2021
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	<StructureSection load='1gpo' size='340' side='right'caption='[[1gpo]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1gpo' size='340' side='right'caption='[[1gpo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1GPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GPO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</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=1gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpo OCA], [~~http~~://pdbe.org/1gpo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1gpo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1gpo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1gpo 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=1gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpo OCA], [https://pdbe.org/1gpo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gpo RCSB], [https://www.ebi.ac.uk/pdbsum/1gpo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gpo ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 29:		Line 29:
	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Sandbox 20009\|Sandbox 20009]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:03, 23 October 2019

OCA — Wed, 23 Oct 2019 09:03:16 GMT

←Older revision		Revision as of 09:03, 23 October 2019
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	==CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT==		==CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT==
-	<StructureSection load='1gpo' size='340' side='right' caption='[[1gpo]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='1gpo' size='340' side='right'caption='[[1gpo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GPO FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GPO FirstGlance]. <br>
Line 28:		Line 28:

	==See Also==		==See Also==
-	*[[3D structures ~~of antibody~~\|3D structures ~~of antibody~~]]	+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Schiweck, W]]		[[Category: Schiweck, W]]

OCA at 06:43, 3 January 2018

OCA — Wed, 03 Jan 2018 06:43:14 GMT

←Older revision		Revision as of 06:43, 3 January 2018
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT==		==CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT==
	<StructureSection load='1gpo' size='340' side='right' caption='[[1gpo]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1gpo' size='340' side='right' caption='[[1gpo]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GPO FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GPO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</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=1gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpo OCA], [http://pdbe.org/1gpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gpo RCSB], [http://www.ebi.ac.uk/pdbsum/1gpo 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=1gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpo OCA], [http://pdbe.org/1gpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gpo RCSB], [http://www.ebi.ac.uk/pdbsum/1gpo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gpo ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/1gpo_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/1gpo_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 27:		Line 28:

	==See Also==		==See Also==
-	*[[~~Antibody~~\|~~Antibody~~]]	+	*[[3D structures of antibody\|3D structures of antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:53, 8 February 2016

OCA — Mon, 08 Feb 2016 18:53:47 GMT

←Older revision		Revision as of 18:53, 8 February 2016
Line 14:		Line 14:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gpo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:26, 10 September 2015

OCA — Thu, 10 Sep 2015 14:26:23 GMT

←Older revision		Revision as of 14:26, 10 September 2015
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	<StructureSection load='1gpo' size='340' side='right' caption='[[1gpo]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1gpo' size='340' side='right' caption='[[1gpo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GPO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</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=1gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gpo RCSB], [http://www.ebi.ac.uk/pdbsum/1gpo 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=1gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpo OCA], [http://pdbe.org/1gpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gpo RCSB], [http://www.ebi.ac.uk/pdbsum/1gpo PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 24:		Line 24:
	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 1gpo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 31:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mus musculus]]~~	+	[[Category: Lk3 transgenic mice]]
-	~~[[Category: Synthetic construct~~]]	+
	[[Category: Schiweck, W]]		[[Category: Schiweck, W]]
	[[Category: Skerra, A]]		[[Category: Skerra, A]]

OCA at 23:07, 22 December 2014

OCA — Mon, 22 Dec 2014 23:07:23 GMT

←Older revision		Revision as of 23:07, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GPO FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GPO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gpo RCSB], [http://www.ebi.ac.uk/pdbsum/1gpo 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=1gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gpo RCSB], [http://www.ebi.ac.uk/pdbsum/1gpo PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Synthetic construct]]		[[Category: Synthetic construct]]
-	[[Category: Schiweck, W.]]	+	[[Category: Schiweck, W]]
-	[[Category: Skerra, A.]]	+	[[Category: Skerra, A]]
	[[Category: Antibody design]]		[[Category: Antibody design]]
	[[Category: Antigen-binding site]]		[[Category: Antigen-binding site]]

OCA at 04:22, 3 October 2014

OCA — Fri, 03 Oct 2014 04:22:03 GMT

←Older revision		Revision as of 04:22, 3 October 2014
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-	~~{{STRUCTURE_1gpo\| PDB=1gpo \| SCENE= }}~~	+	==CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT==
-	===CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT===	+	<StructureSection load='1gpo' size='340' side='right' caption='[[1gpo]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~{{ABSTRACT_PUBMED_9180382}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1gpo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GPO FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gpo RCSB], [http://www.ebi.ac.uk/pdbsum/1gpo PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/1gpo_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In a protein design study the artificial antibody M41 was modelled with its binding site complementary to the protease inhibitor cystatin, which was chosen as a structurally well-characterized "antigen". The modelling of M41 took advantage of the crystal structure of the anti-lysozyme antibody HyHEL-10 as a structural template. Its combining site was reshaped by replacing 19 amino acid side-chains in the hypervariable loops. In addition, ten amino acid residues were substituted in the framework regions. The crystal structure of the corresponding antibody model M41, which was produced as an F(ab) fragment in Escherichia coli, was determined at a resolution of 1.95 A. The crystals exhibited symmetry of the space group P2(1)2(1)2(1) (a = 96.5 A; b = 103.5 A; c = 113.6 A) with two F(ab) fragments in the asymmetric unit, which were independently refined (final R-factor 21.7%). The resulting coordinates were used for a detailed comparison with the modelled protein structure. It was found that the mutual arrangement of the six complementarity-determining regions as well as most of their backbone conformation had been correctly predicted. One major difference that was detected for the conformation of a five residue insertion in complementarity-determining region L1 could be explained by an erroneously defined segment in the structure of the antibody 4-4-20, which had been used as a template for this loop. In the light of more recent crystallographic data it appears that this segment adopts a new canonical structure. Apart from this region, most of the side-chains in the antigen-binding site had been properly placed in the M41 model. There was however one important exception concerning Trp H98, whose side-chain conformation had been kept as it appeared in HyHEL-10. The differing orientation of this residue in the model compared with the crystal structure of the artificial F(ab) fragment M41 explains why an antigen affinity could not be detected so far. The detailed analysis of this and other, more subtle deviations suggests how to make this F(ab) fragment function by introducing a few additional amino acid changes into M41.

-	~~==About this Structure==~~	+	The rational construction of an antibody against cystatin: lessons from the crystal structure of an artificial Fab fragment.,Schiweck W, Skerra A J Mol Biol. 1997 May 23;268(5):934-51. PMID:9180382<ref>PMID:9180382</ref>
-	~~[[1gpo]] is a 4 chain~~ structure ~~with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mus_musculus Mus musculus] and [http~~:~~//en~~.~~wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1GPO OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:009180382</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Antibody\|Antibody]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Synthetic construct]]		[[Category: Synthetic construct]]

OCA at 03:05, 20 September 2013

OCA — Fri, 20 Sep 2013 03:05:05 GMT

←Older revision		Revision as of 03:05, 20 September 2013
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-	[[Image:1gpo.png\|left\|200px]]
-
	{{STRUCTURE_1gpo\| PDB=1gpo \| SCENE= }}		{{STRUCTURE_1gpo\| PDB=1gpo \| SCENE= }}
-
	===CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT===		===CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT===
-
	{{ABSTRACT_PUBMED_9180382}}		{{ABSTRACT_PUBMED_9180382}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:009180382</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009180382</ref><references group="xtra"/><references/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Synthetic construct]]		[[Category: Synthetic construct]]
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	[[Category: Canonical conformation]]		[[Category: Canonical conformation]]
	[[Category: Complementarity-determining region]]		[[Category: Complementarity-determining region]]
-	[[Category: ~~Immunoglobulin~~]]	+	[[Category: Immune system]]
	[[Category: Immunoglobulin structure]]		[[Category: Immunoglobulin structure]]
	[[Category: Protein engineering]]		[[Category: Protein engineering]]

OCA: Protected "1gpo" [edit=sysop:move=sysop]

OCA — Wed, 21 Nov 2012 16:10:28 GMT

Protected "1gpo" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:10, 21 November 2012