3okn - Revision history

OCA at 11:17, 21 February 2024

OCA — Wed, 21 Feb 2024 11:17:13 GMT

←Older revision		Revision as of 11:17, 21 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3okn]] is a 2 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=3OKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OKN FirstGlance]. <br>		<table><tr><td colspan='2'>[[3okn]] is a 2 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=3OKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OKN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~"><~~scene name~~='~~pdbligand~~=ZN:~~ZINC+ION'~~>ZN</~~scene~~>, <scene name='pdbligand=KDA:(3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID)-2-O-ALLYL'>KDA</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</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]] 2.15Å</td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[3okd\|3okd]], [[3oke\|3oke]], [[3okk\|3okk]], [[3mhl\|3mhl]], [[3mhm\|3mhm]], [[3mho\|3mho]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KDA:(3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID)-2-O-ALLYL'>KDA</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okn OCA], [https://pdbe.org/3okn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3okn RCSB], [https://www.ebi.ac.uk/pdbsum/3okn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3okn 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=3okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okn OCA], [https://pdbe.org/3okn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3okn RCSB], [https://www.ebi.ac.uk/pdbsum/3okn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3okn ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structures of the antigen-binding fragment of the murine monoclonal antibody (mAb) S25-39 in the presence of several antigens representing chlamydial lipopolysaccharide (LPS) epitopes based on the bacterial sugar 3-deoxy-alpha-d-manno-oct-2-ulosonic acid (Kdo) have been determined at resolutions from 2.4 to 1.8 A. The antigen-binding site of this antibody differs from the well-characterized antibody S25-2 by a single mutation away from the germline of asparagine H53 to lysine, yet this one mutation results in a significant increase in avidity across a range of antigens. A comparison of the two antibody structures reveals that the mutated Lys H53 forms additional hydrogen bonds and/or charged-residue interactions with the second Kdo residue of every antigen having two or more carbohydrate residues. Significantly, the NH53K mutation results from a single nucleotide substitution in the germline sequence common among a panel of antibodies raised against glycoconjugates containing carbohydrate epitopes of chlamydial LPS. Like S25-2, S25-39 displays significant induced fit of complementarity determining region (CDR) H3 upon antigen binding, with the unliganded structure possessing a conformation distinct from those reported earlier for S25-2. The four different observed conformations for CDR H3 suggest that this CDR has evolved to exploit the recognition potential of a flexible loop while minimizing the associated entropic penalties of binding by adopting a limited number of ordered conformations in the unliganded state. These observations reveal strategies evolved to balance adaptability and specificity in the germline antibody response to carbohydrate antigens.
-
-	A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity.,Blackler RJ, Muller-Loennies S, Brooks CL, Evans DW, Brade L, Kosma P, Brade H, Evans SV Biochemistry. 2011 Apr 1. PMID:21405106<ref>PMID:21405106</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3okn" style="background-color:#fffaf0;"></div>

	==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]]		*[[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: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Blackler~~, R J~~]]	+	[[Category: Blackler RJ]]
-	[[Category: Evans~~, S V]]~~	+	[[Category: Evans SV]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Carbohydrate]]~~	+
-	~~[[Category: Fab]]~~	+
-	~~[[Category: Igg]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 10:46, 18 May 2022

OCA — Wed, 18 May 2022 10:46:52 GMT

←Older revision		Revision as of 10:46, 18 May 2022
Line 3:		Line 3:
	<StructureSection load='3okn' size='340' side='right'caption='[[3okn]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3okn' size='340' side='right'caption='[[3okn]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3okn]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3OKN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3okn]] is a 2 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=3OKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OKN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KDA:(3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID)-2-O-ALLYL'>KDA</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO~~</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=KDA:(3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID)-2-O-ALLYL'>KDA</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3okd\|3okd]], [[3oke\|3oke]], [[3okk\|3okk]], [[3mhl\|3mhl]], [[3mhm\|3mhm]], [[3mho\|3mho]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3okd\|3okd]], [[3oke\|3oke]], [[3okk\|3okk]], [[3mhl\|3mhl]], [[3mhm\|3mhm]], [[3mho\|3mho]]</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=3okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okn OCA], [~~http~~://pdbe.org/3okn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3okn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3okn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3okn 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=3okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okn OCA], [https://pdbe.org/3okn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3okn RCSB], [https://www.ebi.ac.uk/pdbsum/3okn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3okn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	==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 13:40, 25 December 2019

OCA — Wed, 25 Dec 2019 13:40:40 GMT

←Older revision		Revision as of 13:40, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo==		==Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo==
-	<StructureSection load='3okn' size='340' side='right' caption='[[3okn]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='3okn' size='340' side='right'caption='[[3okn]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3okn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OKN FirstGlance]. <br>		<table><tr><td colspan='2'>[[3okn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OKN FirstGlance]. <br>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Blackler, R J]]		[[Category: Blackler, R J]]

OCA at 05:42, 8 March 2018

OCA — Thu, 08 Mar 2018 05:42:33 GMT

←Older revision		Revision as of 05:42, 8 March 2018
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3okn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OKN FirstGlance]. <br>		<table><tr><td colspan='2'>[[3okn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OKN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>,~~ <scene name='pdbligand=KDA:(3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID)-2-O-ALLYL'>KDA</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KDA:(3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID)-2-O-ALLYL'>KDA</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3okd\|3okd]], [[3oke\|3oke]], [[3okk\|3okk]], [[3mhl\|3mhl]], [[3mhm\|3mhm]], [[3mho\|3mho]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3okd\|3okd]], [[3oke\|3oke]], [[3okk\|3okk]], [[3mhl\|3mhl]], [[3mhm\|3mhm]], [[3mho\|3mho]]</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=3okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okn OCA], [http://pdbe.org/3okn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3okn RCSB], [http://www.ebi.ac.uk/pdbsum/3okn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3okn ProSAT]</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=3okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okn OCA], [http://pdbe.org/3okn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3okn RCSB], [http://www.ebi.ac.uk/pdbsum/3okn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3okn ProSAT]</span></td></tr>
Line 19:		Line 19:

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

OCA at 03:57, 10 December 2016

OCA — Sat, 10 Dec 2016 03:57:36 GMT

←Older revision		Revision as of 03:57, 10 December 2016
Line 1:		Line 1:
		+
	==Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo==		==Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo==
	<StructureSection load='3okn' size='340' side='right' caption='[[3okn]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3okn' size='340' side='right' caption='[[3okn]], [[Resolution\|resolution]] 2.15Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=KDA:(3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID)-2-O-ALLYL'>KDA</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=KDA:(3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID)-2-O-ALLYL'>KDA</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3okd\|3okd]], [[3oke\|3oke]], [[3okk\|3okk]], [[3mhl\|3mhl]], [[3mhm\|3mhm]], [[3mho\|3mho]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3okd\|3okd]], [[3oke\|3oke]], [[3okk\|3okk]], [[3mhl\|3mhl]], [[3mhm\|3mhm]], [[3mho\|3mho]]</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=3okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3okn RCSB], [http://www.ebi.ac.uk/pdbsum/3okn 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=3okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okn OCA], [http://pdbe.org/3okn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3okn RCSB], [http://www.ebi.ac.uk/pdbsum/3okn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3okn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 3okn" style="background-color:#fffaf0;"></div>

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

OCA at 11:03, 9 December 2014

OCA — Tue, 09 Dec 2014 11:03:11 GMT

←Older revision		Revision as of 11:03, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3okn.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo==
		+	<StructureSection load='3okn' size='340' side='right' caption='[[3okn]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3okn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OKN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=KDA:(3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID)-2-O-ALLYL'>KDA</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3okd\|3okd]], [[3oke\|3oke]], [[3okk\|3okk]], [[3mhl\|3mhl]], [[3mhm\|3mhm]], [[3mho\|3mho]]</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=3okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3okn RCSB], [http://www.ebi.ac.uk/pdbsum/3okn PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structures of the antigen-binding fragment of the murine monoclonal antibody (mAb) S25-39 in the presence of several antigens representing chlamydial lipopolysaccharide (LPS) epitopes based on the bacterial sugar 3-deoxy-alpha-d-manno-oct-2-ulosonic acid (Kdo) have been determined at resolutions from 2.4 to 1.8 A. The antigen-binding site of this antibody differs from the well-characterized antibody S25-2 by a single mutation away from the germline of asparagine H53 to lysine, yet this one mutation results in a significant increase in avidity across a range of antigens. A comparison of the two antibody structures reveals that the mutated Lys H53 forms additional hydrogen bonds and/or charged-residue interactions with the second Kdo residue of every antigen having two or more carbohydrate residues. Significantly, the NH53K mutation results from a single nucleotide substitution in the germline sequence common among a panel of antibodies raised against glycoconjugates containing carbohydrate epitopes of chlamydial LPS. Like S25-2, S25-39 displays significant induced fit of complementarity determining region (CDR) H3 upon antigen binding, with the unliganded structure possessing a conformation distinct from those reported earlier for S25-2. The four different observed conformations for CDR H3 suggest that this CDR has evolved to exploit the recognition potential of a flexible loop while minimizing the associated entropic penalties of binding by adopting a limited number of ordered conformations in the unliganded state. These observations reveal strategies evolved to balance adaptability and specificity in the germline antibody response to carbohydrate antigens.

-	~~{{STRUCTURE_3okn\| PDB=3okn \| SCENE= }}~~	+	A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity.,Blackler RJ, Muller-Loennies S, Brooks CL, Evans DW, Brade L, Kosma P, Brade H, Evans SV Biochemistry. 2011 Apr 1. PMID:21405106<ref>PMID:21405106</ref>

-	~~===Crystal structure~~ of ~~S25-39 in complex with Kdo(2~~.~~4)Kdo(2~~.~~4)Kdo===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21405106}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3okn]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA].~~	+

	==See Also==		==See Also==
	*[[Antibody\|Antibody]]		*[[Antibody\|Antibody]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:021405106<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Blackler, R J.]]	+	[[Category: Blackler, R J]]
-	[[Category: Evans, S V.]]	+	[[Category: Evans, S V]]
	[[Category: Antibody]]		[[Category: Antibody]]
	[[Category: Carbohydrate]]		[[Category: Carbohydrate]]

OCA at 10:11, 20 October 2012

OCA — Sat, 20 Oct 2012 10:11:01 GMT

←Older revision		Revision as of 10:11, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3okn]] is a 2 chain structure ~~of [[Antibody]]~~ with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA].	+	[[3okn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA].

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

OCA at 01:15, 26 July 2012

OCA — Thu, 26 Jul 2012 01:15:58 GMT

←Older revision		Revision as of 01:15, 26 July 2012
Line 1:		Line 1:
	[[Image:3okn.png\|left\|200px]]		[[Image:3okn.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3okn", 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_3okn\| PDB=3okn \| SCENE= }}		{{STRUCTURE_3okn\| PDB=3okn \| SCENE= }}

	===Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo===		===Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21405106}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21405106 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21405106}}		{{ABSTRACT_PUBMED_21405106}}

	==About this Structure==		==About this Structure==
-	[[3okn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA].	+	[[3okn]] is a 2 chain structure of [[Antibody]] with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA].
		+
		+	==See Also==
		+	*[[Antibody\|Antibody]]

	==Reference==		==Reference==
Line 26:		Line 18:
	[[Category: Blackler, R J.]]		[[Category: Blackler, R J.]]
	[[Category: Evans, S V.]]		[[Category: Evans, S V.]]
		+	[[Category: Antibody]]
		+	[[Category: Carbohydrate]]
		+	[[Category: Fab]]
		+	[[Category: Igg]]
		+	[[Category: Immune system]]

OCA at 06:14, 4 May 2011

OCA — Wed, 04 May 2011 06:14:07 GMT

←Older revision		Revision as of 06:14, 4 May 2011
Line 1:		Line 1:
-	[[Image:3okn.~~jpg~~\|left\|200px]]	+	[[Image:3okn.png\|left\|200px]]

	<!--		<!--
Line 22:		Line 22:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21405106~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021405106</ref><references group="xtra"/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Blackler, R J.]]		[[Category: Blackler, R J.]]
	[[Category: Evans, S V.]]		[[Category: Evans, S V.]]

OCA at 09:03, 6 April 2011

OCA — Wed, 06 Apr 2011 09:03:01 GMT

←Older revision		Revision as of 09:03, 6 April 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3okn.jpg\|left\|200px]]

-	The ~~entry 3okn~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3okn", 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_3okn\| PDB=3okn \| SCENE= }}

-	~~Authors: Blackler, R~~.~~J., Evans, S.V~~.	+	===Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo===

-	~~Description: Crystal structure of S25~~-~~39 in complex with Kdo~~(2.4)~~Kdo(~~2.~~4)Kdo~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21405106}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21405106 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21405106}}
		+
		+	==About this Structure==
		+	[[3okn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKN OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:21405106</ref><references group="xtra"/>
		+	[[Category: Mus musculus]]
		+	[[Category: Blackler, R J.]]
		+	[[Category: Evans, S V.]]