1ri8 - Revision history

OCA at 08:23, 1 May 2024

2024-05-01T08:23:59Z

←Older revision		Revision as of 08:23, 1 May 2024
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	<StructureSection load='1ri8' size='340' side='right'caption='[[1ri8]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1ri8' size='340' side='right'caption='[[1ri8]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arabian_camel Arabian camel~~] and [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius] and [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.85Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=1ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ri8 OCA], [https://pdbe.org/1ri8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ri8 RCSB], [https://www.ebi.ac.uk/pdbsum/1ri8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ri8 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=1ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ri8 OCA], [https://pdbe.org/1ri8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ri8 RCSB], [https://www.ebi.ac.uk/pdbsum/1ri8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ri8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>	+	[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=1ri8 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=1ri8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A central paradigm in immunology states that successful generation of high affinity antibodies necessitates an immense primary repertoire of antigen-combining sites. Much of the diversity of this repertoire is provided by varying one antigen binding loop, created by inserting randomly a D (diversity) gene out of a small pool between the V and J genes. It is therefore assumed that any particular D-encoded region surrounded by different V and J regions adopts a different conformation. We have solved the structure of two lysozyme-specific variable domains of heavy-chain antibodies isolated from two strictly unrelated dromedaries. These antibodies recombined identical D gene sequences to different V and J precursors with significant variance in their V(D)J junctions. Despite these large differences, the D-encoded loop segments adopt remarkably identical architectures, thus directing the antibodies toward identical epitopes. Furthermore, a striking convergent maturation process occurred in the V region, adapting both binders for their sub-nanomolar affinity association with lysozyme. Hence, on a structural level, humoral immunity may rely more on well developed maturation and selection systems than on the acquisition of large primary repertoires.
-
-	Strong in vivo maturation compensates for structurally restricted H3 loops in antibody repertoires.,De Genst E, Silence K, Ghahroudi MA, Decanniere K, Loris R, Kinne J, Wyns L, Muyldermans S J Biol Chem. 2005 Apr 8;280(14):14114-21. Epub 2005 Jan 19. PMID:15659390<ref>PMID:15659390</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ri8" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arabian camel~~]]	+	[[Category: Camelus dromedarius]]
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lysozyme~~]]	+	[[Category: De Genst E]]
-	[[Category: Decanniere, K]]	+	[[Category: Decanniere K]]
-	~~[[Category: Genst, E De~~]]	+	[[Category: Ghahroudi MA]]
-	[[Category: Ghahroudi~~, M A~~]]	+	[[Category: Kinne J]]
-	[[Category: Kinne, J]]	+	[[Category: Loris R]]
-	[[Category: Loris, R]]	+	[[Category: Muyldermans S]]
-	[[Category: Muyldermans, S]]	+	[[Category: Silence K]]
-	[[Category: Silence, K]]	+	[[Category: Wyns L]]
-	[[Category: Wyns, L]]	+
-	~~[[Category: Alpha-beta orthogonal bundle]]~~	+
-	~~[[Category: Beta sandwich]]~~	+
-	~~[[Category: Immune system-hydrolase complex]]~~	+
-	~~[[Category: Immunoglobulin fold]]~~	+
-	~~[[Category: Vhh-lysozyme complex~~]]	+

OCA at 10:13, 15 September 2021

2021-09-15T10:13:41Z

←Older revision		Revision as of 10:13, 15 September 2021
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	<StructureSection load='1ri8' size='340' side='right'caption='[[1ri8]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1ri8' size='340' side='right'caption='[[1ri8]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [~~http~~://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=1ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ri8 OCA], [~~http~~://pdbe.org/1ri8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ri8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ri8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ri8 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=1ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ri8 OCA], [https://pdbe.org/1ri8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ri8 RCSB], [https://www.ebi.ac.uk/pdbsum/1ri8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ri8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>	+	[[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]		*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:39, 4 December 2019

2019-12-04T11:39:04Z

←Older revision		Revision as of 11:39, 4 December 2019
Line 1:		Line 1:

	==Crystal Structure of the Camelid Single Domain Antibody 1D2L19 in complex with Hen Egg White Lysozyme==		==Crystal Structure of the Camelid Single Domain Antibody 1D2L19 in complex with Hen Egg White Lysozyme==
-	<StructureSection load='1ri8' size='340' side='right' caption='[[1ri8]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='1ri8' size='340' side='right'caption='[[1ri8]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>
Line 39:		Line 39:
	[[Category: Arabian camel]]		[[Category: Arabian camel]]
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Decanniere, K]]		[[Category: Decanniere, K]]

OCA at 08:03, 28 February 2018

2018-02-28T08:03:20Z

←Older revision		Revision as of 08:03, 28 February 2018
Line 1:		Line 1:
		+
	==Crystal Structure of the Camelid Single Domain Antibody 1D2L19 in complex with Hen Egg White Lysozyme==		==Crystal Structure of the Camelid Single Domain Antibody 1D2L19 in complex with Hen Egg White Lysozyme==
	<StructureSection load='1ri8' size='340' side='right' caption='[[1ri8]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1ri8' size='340' side='right' caption='[[1ri8]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [http://en.wikipedia.org/wiki/~~Chick Chick~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=1ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ri8 OCA], [http://pdbe.org/1ri8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ri8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ri8 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=1ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ri8 OCA], [http://pdbe.org/1ri8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ri8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ri8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ri8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/1ri8_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/1ri8_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 30:		Line 31:

	==See Also==		==See Also==
-	*[[Antibody\|Antibody]]	+	*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]		*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
Line 37:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Arabian camel]]		[[Category: Arabian camel]]
-	[[Category: ~~Chick~~]]	+	[[Category: Gallus gallus]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Decanniere, K]]		[[Category: Decanniere, K]]

OCA at 23:53, 8 February 2016

2016-02-08T23:53:45Z

←Older revision		Revision as of 23:53, 8 February 2016
Line 17:		Line 17:
	<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=1ri8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:35, 10 September 2015

2015-09-10T16:35:41Z

←Older revision		Revision as of 16:35, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1ri8' size='340' side='right' caption='[[1ri8]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1ri8' size='340' side='right' caption='[[1ri8]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Camelus_dromedarius Camelus dromedarius~~] and [http://en.wikipedia.org/wiki/~~Gallus_gallus Gallus gallus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=1ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ri8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ri8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ri8 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=1ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ri8 OCA], [http://pdbe.org/1ri8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ri8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ri8 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1ri8" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Camelus dromedarius~~]]	+	[[Category: Arabian camel]]
-	[[Category: ~~Gallus gallus~~]]	+	[[Category: Chick]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Decanniere, K]]		[[Category: Decanniere, K]]

OCA at 03:01, 25 December 2014

2014-12-25T03:01:12Z

←Older revision		Revision as of 03:01, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius] and [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius] and [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></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=1ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ri8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ri8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ri8 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=1ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ri8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ri8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ri8 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Decanniere, K.]]	+	[[Category: Decanniere, K]]
-	[[Category: Genst, E De.]]	+	[[Category: Genst, E De]]
-	[[Category: Ghahroudi, M A.]]	+	[[Category: Ghahroudi, M A]]
-	[[Category: Kinne, J.]]	+	[[Category: Kinne, J]]
-	[[Category: Loris, R.]]	+	[[Category: Loris, R]]
-	[[Category: Muyldermans, S.]]	+	[[Category: Muyldermans, S]]
-	[[Category: Silence, K.]]	+	[[Category: Silence, K]]
-	[[Category: Wyns, L.]]	+	[[Category: Wyns, L]]
	[[Category: Alpha-beta orthogonal bundle]]		[[Category: Alpha-beta orthogonal bundle]]
	[[Category: Beta sandwich]]		[[Category: Beta sandwich]]

OCA at 19:46, 28 September 2014

2014-09-28T19:46:28Z

←Older revision		Revision as of 19:46, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1ri8.~~png\|left~~\|200px]]	+	==Crystal Structure of the Camelid Single Domain Antibody 1D2L19 in complex with Hen Egg White Lysozyme==
		+	<StructureSection load='1ri8' size='340' side='right' caption='[[1ri8]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ri8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius] and [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RI8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></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=1ri8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ri8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ri8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ri8 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/ri/1ri8_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 ==
		+	A central paradigm in immunology states that successful generation of high affinity antibodies necessitates an immense primary repertoire of antigen-combining sites. Much of the diversity of this repertoire is provided by varying one antigen binding loop, created by inserting randomly a D (diversity) gene out of a small pool between the V and J genes. It is therefore assumed that any particular D-encoded region surrounded by different V and J regions adopts a different conformation. We have solved the structure of two lysozyme-specific variable domains of heavy-chain antibodies isolated from two strictly unrelated dromedaries. These antibodies recombined identical D gene sequences to different V and J precursors with significant variance in their V(D)J junctions. Despite these large differences, the D-encoded loop segments adopt remarkably identical architectures, thus directing the antibodies toward identical epitopes. Furthermore, a striking convergent maturation process occurred in the V region, adapting both binders for their sub-nanomolar affinity association with lysozyme. Hence, on a structural level, humoral immunity may rely more on well developed maturation and selection systems than on the acquisition of large primary repertoires.

-	~~{{STRUCTURE_1ri8\| PDB=1ri8 \| SCENE= }}~~	+	Strong in vivo maturation compensates for structurally restricted H3 loops in antibody repertoires.,De Genst E, Silence K, Ghahroudi MA, Decanniere K, Loris R, Kinne J, Wyns L, Muyldermans S J Biol Chem. 2005 Apr 8;280(14):14114-21. Epub 2005 Jan 19. PMID:15659390<ref>PMID:15659390</ref>

-	~~===Crystal Structure~~ of the ~~Camelid Single Domain Antibody 1D2L19 in complex with Hen Egg White Lysozyme===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15659390}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ri8]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Camelus_dromedarius Camelus dromedarius] and [http://en~~.~~wikipedia.org~~/~~wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Hen Egg-White (HEW)~~ Lysozyme\|~~Hen Egg-White (HEW)~~ Lysozyme]]	+	*[[Antibody\|Antibody]]
-		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-	==~~Reference~~==	+	== References ==
-	<~~ref group="xtra">PMID:015659390<~~/~~ref~~><~~references group="xtra"~~/>	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Camelus dromedarius]]		[[Category: Camelus dromedarius]]
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]

OCA at 11:54, 20 October 2012

2012-10-20T11:54:24Z

←Older revision		Revision as of 11:54, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ri8]] is a 2 chain structure ~~of [[Hen Egg-White (HEW) Lysozyme]]~~ with sequence from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius] and [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA].	+	[[1ri8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius] and [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RI8 OCA].

	==See Also==		==See Also==

OCA: Protected "1ri8" [edit=sysop:move=sysop]

2012-07-26T06:59:22Z

Protected "1ri8" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:59, 26 July 2012