1g7i - Revision history

OCA at 11:19, 27 March 2024

2024-03-27T11:19:51Z

←Older revision		Revision as of 11:19, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='1g7i' size='340' side='right'caption='[[1g7i]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1g7i' size='340' side='right'caption='[[1g7i]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1g7i]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G7I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1g7i]] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G7I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [https://pdbe.org/1g7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [https://www.ebi.ac.uk/pdbsum/1g7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g7i 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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [https://pdbe.org/1g7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [https://www.ebi.ac.uk/pdbsum/1g7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g7i 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/HVM44_MOUSE HVM44_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=1g7i 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=1g7i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Antigen-antibody complexes provide useful models for analyzing the thermodynamics of protein-protein association reactions. We have employed site-directed mutagenesis, X-ray crystallography, and isothermal titration calorimetry to investigate the role of hydrophobic interactions in stabilizing the complex between the Fv fragment of the anti-hen egg white lysozyme (HEL) antibody D1.3 and HEL. Crystal structures of six FvD1.3-HEL mutant complexes in which an interface tryptophan residue (V(L)W92) has been replaced by residues with smaller side chains (alanine, serine, valine, aspartate, histidine, and phenylalanine) were determined to resolutions between 1.75 and 2.00 A. In the wild-type complex, V(L)W92 occupies a large hydrophobic pocket on the surface of HEL and constitutes an energetic "hot spot" for antigen binding. The losses in apolar buried surface area in the mutant complexes, relative to wild-type, range from 25 (V(L)F92) to 115 A(2) (V(L)A92), with no significant shifts in the positions of protein atoms at the mutation site for any of the complexes except V(L)A92, where there is a peptide flip. The affinities of the mutant Fv fragments for HEL are 10-100-fold lower than that of the original antibody. Formation of all six mutant complexes is marked by a decrease in binding enthalpy that exceeds the decrease in binding free energy, such that the loss in enthalpy is partly offset by a compensating gain in entropy. No correlation was observed between decreases in apolar, polar, or aggregate (sum of the apolar and polar) buried surface area in the V(L)92 mutant series and changes in the enthalpy of formation. Conversely, there exist linear correlations between losses of apolar buried surface and decreases in binding free energy (R(2) = 0.937) as well as increases in the solvent portion of the entropy of binding (R(2) = 0.909). The correlation between binding free energy and apolar buried surface area corresponds to 21 cal mol(-1) A(-2) (1 cal = 4.185 J) for the effective hydrophobicity at the V(L)92 mutation site. Furthermore, the slope of the line defined by the correlation between changes in binding free energy and solvent entropy approaches unity, demonstrating that the exclusion of solvent from the binding interface is the predominant energetic factor in the formation of this protein complex. Our estimate of the hydrophobic contribution to binding at site V(L)92 in the D1.3-HEL interface is consistent with values for the hydrophobic effect derived from classical hydrocarbon solubility models. We also show how residue V(L)W92 can contribute significantly less to stabilization when buried in a more polar pocket, illustrating the dependence of the hydrophobic effect on local environment at different sites in a protein-protein interface.
-
-	Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface.,Sundberg EJ, Urrutia M, Braden BC, Isern J, Tsuchiya D, Fields BA, Malchiodi EL, Tormo J, Schwarz FP, Mariuzza RA Biochemistry. 2000 Dec 19;39(50):15375-87. PMID:11112523<ref>PMID:11112523</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1g7i" 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: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice]]~~	+	[[Category: Mus musculus]]
-	~~[[Category: Lysozyme~~]]	+	[[Category: Braden BC]]
-	[[Category: Braden~~, B C~~]]	+	[[Category: Isern J]]
-	[[Category: Isern, J]]	+	[[Category: Mariuzza RA]]
-	[[Category: Mariuzza~~, R A~~]]	+	[[Category: Sundberg EJ]]
-	[[Category: Sundberg~~, E J~~]]	+	[[Category: Urrutia M]]
-	[[Category: Urrutia, M]]	+
-	~~[[Category: Hydrolase inhibitor-hydrolase complex]]~~	+
-	~~[[Category: Hydrolase inhibitor/hydrolase~~]]	+

OCA at 07:12, 24 March 2021

2021-03-24T07:12:39Z

←Older revision		Revision as of 07:12, 24 March 2021
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	<StructureSection load='1g7i' size='340' side='right'caption='[[1g7i]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1g7i' size='340' side='right'caption='[[1g7i]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1g7i]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1G7I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1g7i]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G7I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [~~http~~://pdbe.org/1g7i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1g7i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1g7i 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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [https://pdbe.org/1g7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [https://www.ebi.ac.uk/pdbsum/1g7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g7i 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 06:53, 19 June 2019

2019-06-19T06:53:13Z

←Older revision		Revision as of 06:53, 19 June 2019
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	==CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92F)==		==CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92F)==
-	<StructureSection load='1g7i' size='340' side='right' caption='[[1g7i]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1g7i' size='340' side='right'caption='[[1g7i]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1g7i]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G7I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1g7i]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G7I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</td></tr>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g7/1g7i_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g7/1g7i_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 33:		Line 33:
	==See Also==		==See Also==
	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]		*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-	*[[3D structures ~~of monoclonal antibody~~\|3D structures ~~of monoclonal antibody~~]]	+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Braden, B C]]		[[Category: Braden, B C]]

OCA at 10:46, 13 September 2017

2017-09-13T10:46:19Z

←Older revision		Revision as of 10:46, 13 September 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92F)==		==CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92F)==
	<StructureSection load='1g7i' size='340' side='right' caption='[[1g7i]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1g7i' size='340' side='right' caption='[[1g7i]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1g7i]] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G7I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1g7i]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G7I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [http://pdbe.org/1g7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [http://www.ebi.ac.uk/pdbsum/1g7i 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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [http://pdbe.org/1g7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [http://www.ebi.ac.uk/pdbsum/1g7i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1g7i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=1g7i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 32:		Line 33:
	==See Also==		==See Also==
	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]		*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-	*[[~~Monoclonal Antibody~~\|~~Monoclonal Antibody~~]]	+	*[[3D structures of monoclonal antibody\|3D structures of monoclonal antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chick]]~~	+	[[Category: Gallus gallus]]
-	~~[[Category: Lk3 transgenic mice~~]]	+
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Braden, B C]]		[[Category: Braden, B C]]

OCA at 15:49, 11 September 2015

2015-09-11T15:49:10Z

←Older revision		Revision as of 15:49, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1g7i' size='340' side='right' caption='[[1g7i]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1g7i' size='340' side='right' caption='[[1g7i]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1g7i]] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G7I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1g7i]] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G7I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [http://www.ebi.ac.uk/pdbsum/1g7i 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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [http://pdbe.org/1g7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [http://www.ebi.ac.uk/pdbsum/1g7i PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1g7i" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]		*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
		+	*[[Monoclonal Antibody\|Monoclonal Antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Gallus gallus~~]]	+	[[Category: Chick]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Mus musculus]]
	[[Category: Braden, B C]]		[[Category: Braden, B C]]
	[[Category: Isern, J]]		[[Category: Isern, J]]

OCA at 18:36, 25 December 2014

2014-12-25T18:36:31Z

←Older revision		Revision as of 18:36, 25 December 2014
Line 8:		Line 8:
	<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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [http://www.ebi.ac.uk/pdbsum/1g7i 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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [http://www.ebi.ac.uk/pdbsum/1g7i 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]]

OCA at 00:11, 23 December 2014

2014-12-23T00:11:20Z

←Older revision		Revision as of 00:11, 23 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1g7i]] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G7I FirstGlance]. <br>		<table><tr><td colspan='2'>[[1g7i]] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G7I FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [http://www.ebi.ac.uk/pdbsum/1g7i 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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [http://www.ebi.ac.uk/pdbsum/1g7i PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Braden, B C.]]	+	[[Category: Braden, B C]]
-	[[Category: Isern, J.]]	+	[[Category: Isern, J]]
-	[[Category: Mariuzza, R A.]]	+	[[Category: Mariuzza, R A]]
-	[[Category: Sundberg, E J.]]	+	[[Category: Sundberg, E J]]
-	[[Category: Urrutia, M.]]	+	[[Category: Urrutia, M]]
	[[Category: Hydrolase inhibitor-hydrolase complex]]		[[Category: Hydrolase inhibitor-hydrolase complex]]
	[[Category: Hydrolase inhibitor/hydrolase]]		[[Category: Hydrolase inhibitor/hydrolase]]

OCA at 13:58, 28 September 2014

2014-09-28T13:58:20Z

←Older revision		Revision as of 13:58, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1g7i.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92F)==
		+	<StructureSection load='1g7i' size='340' side='right' caption='[[1g7i]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1g7i]] 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=1G7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G7I FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vfb\|1vfb]], [[1g7h\|1g7h]], [[1g7j\|1g7j]], [[1g7l\|1g7l]], [[1g7m\|1g7m]]</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=1g7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1g7i RCSB], [http://www.ebi.ac.uk/pdbsum/1g7i 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/g7/1g7i_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 ==
		+	Antigen-antibody complexes provide useful models for analyzing the thermodynamics of protein-protein association reactions. We have employed site-directed mutagenesis, X-ray crystallography, and isothermal titration calorimetry to investigate the role of hydrophobic interactions in stabilizing the complex between the Fv fragment of the anti-hen egg white lysozyme (HEL) antibody D1.3 and HEL. Crystal structures of six FvD1.3-HEL mutant complexes in which an interface tryptophan residue (V(L)W92) has been replaced by residues with smaller side chains (alanine, serine, valine, aspartate, histidine, and phenylalanine) were determined to resolutions between 1.75 and 2.00 A. In the wild-type complex, V(L)W92 occupies a large hydrophobic pocket on the surface of HEL and constitutes an energetic "hot spot" for antigen binding. The losses in apolar buried surface area in the mutant complexes, relative to wild-type, range from 25 (V(L)F92) to 115 A(2) (V(L)A92), with no significant shifts in the positions of protein atoms at the mutation site for any of the complexes except V(L)A92, where there is a peptide flip. The affinities of the mutant Fv fragments for HEL are 10-100-fold lower than that of the original antibody. Formation of all six mutant complexes is marked by a decrease in binding enthalpy that exceeds the decrease in binding free energy, such that the loss in enthalpy is partly offset by a compensating gain in entropy. No correlation was observed between decreases in apolar, polar, or aggregate (sum of the apolar and polar) buried surface area in the V(L)92 mutant series and changes in the enthalpy of formation. Conversely, there exist linear correlations between losses of apolar buried surface and decreases in binding free energy (R(2) = 0.937) as well as increases in the solvent portion of the entropy of binding (R(2) = 0.909). The correlation between binding free energy and apolar buried surface area corresponds to 21 cal mol(-1) A(-2) (1 cal = 4.185 J) for the effective hydrophobicity at the V(L)92 mutation site. Furthermore, the slope of the line defined by the correlation between changes in binding free energy and solvent entropy approaches unity, demonstrating that the exclusion of solvent from the binding interface is the predominant energetic factor in the formation of this protein complex. Our estimate of the hydrophobic contribution to binding at site V(L)92 in the D1.3-HEL interface is consistent with values for the hydrophobic effect derived from classical hydrocarbon solubility models. We also show how residue V(L)W92 can contribute significantly less to stabilization when buried in a more polar pocket, illustrating the dependence of the hydrophobic effect on local environment at different sites in a protein-protein interface.

-	~~{{STRUCTURE_1g7i\| PDB=1g7i \| SCENE= }}~~	+	Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface.,Sundberg EJ, Urrutia M, Braden BC, Isern J, Tsuchiya D, Fields BA, Malchiodi EL, Tormo J, Schwarz FP, Mariuzza RA Biochemistry. 2000 Dec 19;39(50):15375-87. PMID:11112523<ref>PMID:11112523</ref>

-	~~===CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92F)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11112523}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1g7i]] 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=1G7I OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Hen Egg-White (HEW)~~ Lysozyme\|~~Hen Egg-White (HEW)~~ Lysozyme]]	+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011112523<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 20:04, 20 October 2012

2012-10-20T20:04:26Z

←Older revision		Revision as of 20:04, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1g7i]] 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=1G7I OCA].	+	[[1g7i]] 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=1G7I OCA].

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

OCA: Protected "1g7i" [edit=sysop:move=sysop]

2012-07-27T09:19:50Z

Protected "1g7i" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:19, 27 July 2012