1nbz - Revision history

OCA at 08:47, 10 April 2024

OCA — Wed, 10 Apr 2024 08:47:52 GMT

←Older revision		Revision as of 08:47, 10 April 2024
Line 3:		Line 3:
	<StructureSection load='1nbz' size='340' side='right'caption='[[1nbz]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1nbz' size='340' side='right'caption='[[1nbz]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nbz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Chick Chick~~] and [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=1NBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nbz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NBZ FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>[[1dqj\|1dqj]]~~, [[~~1dqq~~\|~~1dqq~~]]~~, [[1dqm\|1dqm]], [[1nby\|1nby]], [[1ndg\|1ndg]], [[1ndm\|1ndm]]</div></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbz OCA], [https://pdbe.org/1nbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nbz RCSB], [https://www.ebi.ac.uk/pdbsum/1nbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nbz 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=1nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbz OCA], [https://pdbe.org/1nbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nbz RCSB], [https://www.ebi.ac.uk/pdbsum/1nbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nbz 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/Q569W9_MOUSE Q569W9_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=1nbz 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=1nbz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Alanine-scanning mutagenesis, X-ray crystallography, and double mutant cycles were used to characterize the interface between the anti-hen egg white lysozyme (HEL) antibody HyHEL-63 and HEL. Eleven HEL residues in contact with HyHEL-63 in the crystal structure of the antigen-antibody complex, and 10 HyHEL-63 residues in contact with HEL, were individually truncated to alanine in order to determine their relative contributions to complex stabilization. The residues of HEL (Tyr20, Lys96, and Lys97) most important for binding HyHEL-63 (Delta G(mutant) - Delta G(wild type) > 3.0 kcal/mol) form a contiguous patch at the center of the surface contacted by the antibody. Hot spot residues of the antibody (Delta Delta G > 2.0 kcal/mol) are organized in two clusters that juxtapose hot spot residues of HEL, resulting in energetic complementarity across the interface. All energetically critical residues are centrally located, shielded from solvent by peripheral residues that contribute significantly less to the binding free energy. Although HEL hot spot residues Lys96 and Lys97 make similar interactions with antibody in the HyHEL-63/HEL complex, alanine substitution of Lys96 results in a nearly 100-fold greater reduction in affinity than the corresponding mutation in Lys97. To understand the basis for this marked difference, we determined the crystal structures of the HyHEL-63/HEL Lys96Ala and HyHEL-63/HEL Lys97Ala complexes to 1.80 and 1.85 A resolution, respectively. Whereas conformational changes in the proteins and differences in the solvent networks at the mutation sites appear too small to explain the observed affinity difference, superposition of free HEL in different crystal forms onto bound HEL in the wild type and mutant HyHEL-63/HEL complexes reveals that the side-chain conformation of Lys96 is very similar in the various structures, but that the Lys97 side chain displays considerable flexibility. Accordingly, a greater entropic penalty may be associated with quenching the mobility of the Lys97 than the Lys96 side chain upon complex formation, reducing binding. To further dissect the energetics of specific interactions in the HyHEL-63/HEL interface, double mutant cycles were constructed to measure the coupling of 13 amino acid pairs, 11 of which are in direct contact in the crystal structure. A large coupling energy, 3.0 kcal/mol, was found between HEL residue Lys97 and HyHEL-63 residue V(H)Asp32, which form a buried salt bridge surrounded by polar residues of the antigen. Thus, in contrast to protein folding where buried salt bridges are generally destabilizing, salt bridges in protein-protein interfaces, whose residual composition is more hydrophilic than that of protein interiors, may contribute significantly to complex stabilization.
-
-	Dissection of binding interactions in the complex between the anti-lysozyme antibody HyHEL-63 and its antigen.,Li Y, Urrutia M, Smith-Gill SJ, Mariuzza RA Biochemistry. 2003 Jan 14;42(1):11-22. PMID:12515535<ref>PMID:12515535</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1nbz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]		*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]		*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chick~~]]	+	[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice]]~~	+	[[Category: Mus musculus]]
-	~~[[Category: Lysozyme~~]]	+	[[Category: Li Y]]
-	[[Category: Li, Y]]	+	[[Category: Mariuzza RA]]
-	[[Category: Mariuzza~~, R A~~]]	+	[[Category: Smith-Gill SJ]]
-	[[Category: Smith-Gill~~, S J~~]]	+	[[Category: Urrutia M]]
-	[[Category: Urrutia, M]]	+
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Immune system-hydrolase complex]]~~	+
-	~~[[Category: Mutant~~]]	+

OCA at 07:00, 25 August 2021

OCA — Wed, 25 Aug 2021 07:00:44 GMT

←Older revision		Revision as of 07:00, 25 August 2021
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	<StructureSection load='1nbz' size='340' side='right'caption='[[1nbz]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1nbz' size='340' side='right'caption='[[1nbz]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nbz]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Chick Chick] and [~~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=1NBZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nbz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Chick Chick] and [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=1NBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NBZ FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqj\|1dqj]], [[1dqq\|1dqq]], [[1dqm\|1dqm]], [[1nby\|1nby]], [[1ndg\|1ndg]], [[1ndm\|1ndm]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dqj\|1dqj]], [[1dqq\|1dqq]], [[1dqm\|1dqm]], [[1nby\|1nby]], [[1ndg\|1ndg]], [[1ndm\|1ndm]]</div></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=1nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbz OCA], [~~http~~://pdbe.org/1nbz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1nbz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1nbz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1nbz 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=1nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbz OCA], [https://pdbe.org/1nbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nbz RCSB], [https://www.ebi.ac.uk/pdbsum/1nbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nbz 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]]

OCA at 18:17, 20 November 2019

OCA — Wed, 20 Nov 2019 18:17:39 GMT

←Older revision		Revision as of 18:17, 20 November 2019
Line 1:		Line 1:

	==Crystal Structure of HyHEL-63 complexed with HEL mutant K97A==		==Crystal Structure of HyHEL-63 complexed with HEL mutant K97A==
-	<StructureSection load='1nbz' size='340' side='right' caption='[[1nbz]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='1nbz' size='340' side='right'caption='[[1nbz]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nbz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick] and [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=1NBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NBZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nbz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick] and [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=1NBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NBZ FirstGlance]. <br>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1nbz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nbz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Chick]]		[[Category: Chick]]
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 07:06, 7 February 2018

OCA — Wed, 07 Feb 2018 07:06:39 GMT

←Older revision		Revision as of 07:06, 7 February 2018
Line 1:		Line 1:
		+
	==Crystal Structure of HyHEL-63 complexed with HEL mutant K97A==		==Crystal Structure of HyHEL-63 complexed with HEL mutant K97A==
	<StructureSection load='1nbz' size='340' side='right' caption='[[1nbz]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1nbz' size='340' side='right' caption='[[1nbz]], [[Resolution\|resolution]] 1.85Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqj\|1dqj]], [[1dqq\|1dqq]], [[1dqm\|1dqm]], [[1nby\|1nby]], [[1ndg\|1ndg]], [[1ndm\|1ndm]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqj\|1dqj]], [[1dqq\|1dqq]], [[1dqm\|1dqm]], [[1nby\|1nby]], [[1ndg\|1ndg]], [[1ndm\|1ndm]]</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=1nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbz OCA], [http://pdbe.org/1nbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nbz RCSB], [http://www.ebi.ac.uk/pdbsum/1nbz 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=1nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbz OCA], [http://pdbe.org/1nbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nbz RCSB], [http://www.ebi.ac.uk/pdbsum/1nbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nbz 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/nb/1nbz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nb/1nbz_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 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1nbz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nbz" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-	*[[Monoclonal Antibody\|Monoclonal Antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:44, 8 February 2016

OCA — Mon, 08 Feb 2016 12:44:48 GMT

←Older revision		Revision as of 12:44, 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=1nbz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:42, 10 September 2015

OCA — Thu, 10 Sep 2015 11:42:39 GMT

←Older revision		Revision as of 11:42, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1nbz' size='340' side='right' caption='[[1nbz]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1nbz' size='340' side='right' caption='[[1nbz]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nbz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Gallus_gallus Gallus gallus~~] and [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nbz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick] and [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=1NBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NBZ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqj\|1dqj]], [[1dqq\|1dqq]], [[1dqm\|1dqm]], [[1nby\|1nby]], [[1ndg\|1ndg]], [[1ndm\|1ndm]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqj\|1dqj]], [[1dqq\|1dqq]], [[1dqm\|1dqm]], [[1nby\|1nby]], [[1ndg\|1ndg]], [[1ndm\|1ndm]]</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=1nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nbz RCSB], [http://www.ebi.ac.uk/pdbsum/1nbz 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=1nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbz OCA], [http://pdbe.org/1nbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nbz RCSB], [http://www.ebi.ac.uk/pdbsum/1nbz 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 1nbz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Gallus gallus~~]]	+	[[Category: Chick]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Mus musculus]]
	[[Category: Li, Y]]		[[Category: Li, Y]]
	[[Category: Mariuzza, R A]]		[[Category: Mariuzza, R A]]

OCA at 23:24, 24 December 2014

OCA — Wed, 24 Dec 2014 23:24:38 GMT

←Older revision		Revision as of 23:24, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nbz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NBZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nbz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NBZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqj\|1dqj]], [[1dqq\|1dqq]], [[1dqm\|1dqm]], [[1nby\|1nby]], [[1ndg\|1ndg]], [[1ndm\|1ndm]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqj\|1dqj]], [[1dqq\|1dqq]], [[1dqm\|1dqm]], [[1nby\|1nby]], [[1ndg\|1ndg]], [[1ndm\|1ndm]]</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=1nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nbz RCSB], [http://www.ebi.ac.uk/pdbsum/1nbz 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=1nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nbz RCSB], [http://www.ebi.ac.uk/pdbsum/1nbz 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: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Li, Y.]]	+	[[Category: Li, Y]]
-	[[Category: Mariuzza, R A.]]	+	[[Category: Mariuzza, R A]]
-	[[Category: Smith-Gill, S J.]]	+	[[Category: Smith-Gill, S J]]
-	[[Category: Urrutia, M.]]	+	[[Category: Urrutia, M]]
	[[Category: Antibody]]		[[Category: Antibody]]
	[[Category: Immune system-hydrolase complex]]		[[Category: Immune system-hydrolase complex]]
-	[[Category: Lysozyme]]
	[[Category: Mutant]]		[[Category: Mutant]]

OCA at 14:17, 28 September 2014

OCA — Sun, 28 Sep 2014 14:17:55 GMT

←Older revision		Revision as of 14:17, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1nbz.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of HyHEL-63 complexed with HEL mutant K97A==
		+	<StructureSection load='1nbz' size='340' side='right' caption='[[1nbz]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1nbz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NBZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqj\|1dqj]], [[1dqq\|1dqq]], [[1dqm\|1dqm]], [[1nby\|1nby]], [[1ndg\|1ndg]], [[1ndm\|1ndm]]</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nbz RCSB], [http://www.ebi.ac.uk/pdbsum/1nbz 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/nb/1nbz_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 ==
		+	Alanine-scanning mutagenesis, X-ray crystallography, and double mutant cycles were used to characterize the interface between the anti-hen egg white lysozyme (HEL) antibody HyHEL-63 and HEL. Eleven HEL residues in contact with HyHEL-63 in the crystal structure of the antigen-antibody complex, and 10 HyHEL-63 residues in contact with HEL, were individually truncated to alanine in order to determine their relative contributions to complex stabilization. The residues of HEL (Tyr20, Lys96, and Lys97) most important for binding HyHEL-63 (Delta G(mutant) - Delta G(wild type) > 3.0 kcal/mol) form a contiguous patch at the center of the surface contacted by the antibody. Hot spot residues of the antibody (Delta Delta G > 2.0 kcal/mol) are organized in two clusters that juxtapose hot spot residues of HEL, resulting in energetic complementarity across the interface. All energetically critical residues are centrally located, shielded from solvent by peripheral residues that contribute significantly less to the binding free energy. Although HEL hot spot residues Lys96 and Lys97 make similar interactions with antibody in the HyHEL-63/HEL complex, alanine substitution of Lys96 results in a nearly 100-fold greater reduction in affinity than the corresponding mutation in Lys97. To understand the basis for this marked difference, we determined the crystal structures of the HyHEL-63/HEL Lys96Ala and HyHEL-63/HEL Lys97Ala complexes to 1.80 and 1.85 A resolution, respectively. Whereas conformational changes in the proteins and differences in the solvent networks at the mutation sites appear too small to explain the observed affinity difference, superposition of free HEL in different crystal forms onto bound HEL in the wild type and mutant HyHEL-63/HEL complexes reveals that the side-chain conformation of Lys96 is very similar in the various structures, but that the Lys97 side chain displays considerable flexibility. Accordingly, a greater entropic penalty may be associated with quenching the mobility of the Lys97 than the Lys96 side chain upon complex formation, reducing binding. To further dissect the energetics of specific interactions in the HyHEL-63/HEL interface, double mutant cycles were constructed to measure the coupling of 13 amino acid pairs, 11 of which are in direct contact in the crystal structure. A large coupling energy, 3.0 kcal/mol, was found between HEL residue Lys97 and HyHEL-63 residue V(H)Asp32, which form a buried salt bridge surrounded by polar residues of the antigen. Thus, in contrast to protein folding where buried salt bridges are generally destabilizing, salt bridges in protein-protein interfaces, whose residual composition is more hydrophilic than that of protein interiors, may contribute significantly to complex stabilization.

-	~~{{STRUCTURE_1nbz\| PDB=1nbz \| SCENE= }}~~	+	Dissection of binding interactions in the complex between the anti-lysozyme antibody HyHEL-63 and its antigen.,Li Y, Urrutia M, Smith-Gill SJ, Mariuzza RA Biochemistry. 2003 Jan 14;42(1):11-22. PMID:12515535<ref>PMID:12515535</ref>

-	~~===Crystal Structure~~ of ~~HyHEL-63 complexed with HEL mutant K97A===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12515535}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1nbz]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Gallus_gallus Gallus gallus] and [http://en~~.~~wikipedia.org~~/~~wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NBZ OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Hen Egg-White (HEW)~~ Lysozyme\|~~Hen Egg-White (HEW)~~ Lysozyme]]	+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-		+	*[[Monoclonal Antibody\|Monoclonal Antibody]]
-	==~~Reference~~==	+	== References ==
-	<~~ref group="xtra">PMID:012515535<~~/~~ref~~><~~references group="xtra"~~/>	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 10:10, 20 October 2012

OCA — Sat, 20 Oct 2012 10:10:31 GMT

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

	==About this Structure==		==About this Structure==
-	[[1nbz]] is a 3 chain structure ~~of [[Hen Egg-White (HEW) Lysozyme]]~~ with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NBZ OCA].	+	[[1nbz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NBZ OCA].

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

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

OCA — Thu, 26 Jul 2012 01:14:50 GMT

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

←Older revision

Revision as of 01:14, 26 July 2012