1d5i - Revision history

OCA at 15:46, 13 March 2024

2024-03-13T15:46:33Z

←Older revision		Revision as of 15:46, 13 March 2024
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	<StructureSection load='1d5i' size='340' side='right'caption='[[1d5i]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1d5i' size='340' side='right'caption='[[1d5i]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=1D5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D5I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CD:CADMIUM+ION'>CD</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1axs\|1axs]], [[1d5b\|1d5b]], [[1d6v\|1d6v]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</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=1d5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5i OCA], [https://pdbe.org/1d5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d5i RCSB], [https://www.ebi.ac.uk/pdbsum/1d5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d5i 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=1d5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5i OCA], [https://pdbe.org/1d5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d5i RCSB], [https://www.ebi.ac.uk/pdbsum/1d5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d5i ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/IGKC_HUMAN IGKC_HUMAN] Defects in IGKC are the cause of immunoglobulin kappa light chain deficiency (IGKCD) [MIM:[https://omim.org/entry/614102 614102]. IGKCD is a disease characterized by the complete absence of immunoglobulin kappa chains.<ref>PMID:3931219</ref>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/IGKC_HUMAN IGKC_HUMAN]
	== 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=1d5i 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=1d5i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Antibody AZ-28 was generated against the chairlike transition-state analogue (TSA) 1 and catalyzes the oxy-Cope rearrangement of substrate 2 to product 3. The germline precursor to AZ-28 catalyzes the reaction with a 35-fold higher rate (k(cat)/k(uncat) = 163 000), despite a 40-fold lower binding affinity for TSA.1 (K(D) = 670 nM). To determine the structural basis for the differences in the binding and catalytic properties of the germline and affinity-matured antibodies, the X-ray crystal structures of the unliganded and TSA.1 complex of antibody AZ-28 have been determined at 2.8 and 2.6 A resolution, respectively; the structures of the unliganded and TSA.1 complex of the germline precursor to AZ-28 were both determined at 2. 0 A resolution. In the affinity-matured antibody.hapten complex the TSA is fixed in a catalytically unfavorable conformation by a combination of van der Waals and hydrogen-bonding interactions. The 2- and 5-phenyl substituents of TSA.1 are almost perpendicular to the cyclohexyl ring, leading to decreased orbital overlap and decreased stabilization of the putative transition state. The active site of the germline antibody appears to have an increased degree of flexibility-CDRH3 moves 4.9 A outward from the active site upon binding of TSA.1. We suggest that this conformational flexibility in the germline antibody, which results in a lower binding affinity for TSA.1, allows dynamic changes in the dihedral angle of the 2-phenyl substituent along the reaction coordinate. These conformational changes in turn lead to enhanced orbital overlap and increased catalytic rate. These studies suggest that protein and substrate dynamics play a key role in this antibody-catalyzed reaction.
-
-	Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement.,Mundorff EC, Hanson MA, Varvak A, Ulrich H, Schultz PG, Stevens RC Biochemistry. 2000 Feb 1;39(4):627-32. PMID:10651626<ref>PMID:10651626</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1d5i" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Hanson, M A~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Mundorff, E C~~]]	+	[[Category: Hanson MA]]
-	[[Category: ~~Schultz, P G~~]]	+	[[Category: Mundorff EC]]
-	[[Category: ~~Stevens, R C~~]]	+	[[Category: Schultz PG]]
-	[[Category: ~~Immune system~~]]	+	[[Category: Stevens RC]]

OCA at 09:49, 26 May 2021

2021-05-26T09:49:09Z

←Older revision		Revision as of 09:49, 26 May 2021
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	<StructureSection load='1d5i' size='340' side='right'caption='[[1d5i]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1d5i' size='340' side='right'caption='[[1d5i]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1D5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D5I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1axs\|1axs]], [[1d5b\|1d5b]], [[1d6v\|1d6v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1axs\|1axs]], [[1d5b\|1d5b]], [[1d6v\|1d6v]]</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=1d5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5i OCA], [~~http~~://pdbe.org/1d5i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1d5i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1d5i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1d5i 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=1d5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5i OCA], [https://pdbe.org/1d5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d5i RCSB], [https://www.ebi.ac.uk/pdbsum/1d5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d5i ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:09, 21 August 2019

2019-08-21T07:09:54Z

←Older revision		Revision as of 07:09, 21 August 2019
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	==UNLIGANDED GERMLINE PRECURSOR OF AN OXY-COPE CATALYTIC ANTIBODY==		==UNLIGANDED GERMLINE PRECURSOR OF AN OXY-COPE CATALYTIC ANTIBODY==
-	<StructureSection load='1d5i' size='340' side='right' caption='[[1d5i]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1d5i' size='340' side='right'caption='[[1d5i]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D5I FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D5I FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d5/1d5i_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d5/1d5i_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 29:		Line 29:

	==See Also==		==See Also==
-	*[[3D structures ~~of monoclonal antibody~~\|3D structures ~~of monoclonal antibody~~]]	+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Hanson, M A]]		[[Category: Hanson, M A]]
	[[Category: Mundorff, E C]]		[[Category: Mundorff, E C]]

OCA at 10:23, 3 August 2017

2017-08-03T10:23:44Z

←Older revision		Revision as of 10:23, 3 August 2017
Line 1:		Line 1:
		+
	==UNLIGANDED GERMLINE PRECURSOR OF AN OXY-COPE CATALYTIC ANTIBODY==		==UNLIGANDED GERMLINE PRECURSOR OF AN OXY-COPE CATALYTIC ANTIBODY==
	<StructureSection load='1d5i' size='340' side='right' caption='[[1d5i]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1d5i' size='340' side='right' caption='[[1d5i]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D5I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1axs\|1axs]], [[1d5b\|1d5b]], [[1d6v\|1d6v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1axs\|1axs]], [[1d5b\|1d5b]], [[1d6v\|1d6v]]</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=1d5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5i OCA], [http://pdbe.org/1d5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d5i RCSB], [http://www.ebi.ac.uk/pdbsum/1d5i 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=1d5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5i OCA], [http://pdbe.org/1d5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d5i RCSB], [http://www.ebi.ac.uk/pdbsum/1d5i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d5i ProSAT]</span></td></tr>
	</table>		</table>
-	== Disease ==
-	[[http://www.uniprot.org/uniprot/IGKC_HUMAN IGKC_HUMAN]] Defects in IGKC are the cause of immunoglobulin kappa light chain deficiency (IGKCD) [MIM:[http://omim.org/entry/614102 614102]]. IGKCD is a disease characterized by the complete absence of immunoglobulin kappa chains.<ref>PMID:3931219</ref> [[http://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[http://omim.org/entry/254500 254500]]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 29:

	==See Also==		==See Also==
-	*[[~~Monoclonal Antibody~~\|~~Monoclonal Antibody~~]]	+	*[[3D structures of monoclonal antibody\|3D structures of monoclonal antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Lk3 transgenic mice]]
	[[Category: Hanson, M A]]		[[Category: Hanson, M A]]
	[[Category: Mundorff, E C]]		[[Category: Mundorff, E C]]

OCA at 07:24, 9 February 2016

2016-02-09T07:24:11Z

←Older revision		Revision as of 07:24, 9 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=1d5i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:56, 10 September 2015

2015-09-10T19:56:33Z

←Older revision		Revision as of 19:56, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1d5i' size='340' side='right' caption='[[1d5i]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1d5i' size='340' side='right' caption='[[1d5i]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens] 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=1D5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D5I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1axs\|1axs]], [[1d5b\|1d5b]], [[1d6v\|1d6v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1axs\|1axs]], [[1d5b\|1d5b]], [[1d6v\|1d6v]]</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=1d5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d5i RCSB], [http://www.ebi.ac.uk/pdbsum/1d5i 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=1d5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5i OCA], [http://pdbe.org/1d5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d5i RCSB], [http://www.ebi.ac.uk/pdbsum/1d5i PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
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 1d5i" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens]]~~	+	[[Category: Lk3 transgenic mice]]
-	~~[[Category: Mus musculus~~]]	+
	[[Category: Hanson, M A]]		[[Category: Hanson, M A]]
	[[Category: Mundorff, E C]]		[[Category: Mundorff, E C]]

OCA at 05:20, 25 December 2014

2014-12-25T05:20:17Z

←Older revision		Revision as of 05:20, 25 December 2014
Line 9:		Line 9:
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/IGKC_HUMAN IGKC_HUMAN]] Defects in IGKC are the cause of immunoglobulin kappa light chain deficiency (IGKCD) [MIM:[http://omim.org/entry/614102 614102]]. IGKCD is a disease characterized by the complete absence of immunoglobulin kappa chains.<ref>PMID:3931219</ref> [[http://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[http://omim.org/entry/254500 254500]]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.		[[http://www.uniprot.org/uniprot/IGKC_HUMAN IGKC_HUMAN]] Defects in IGKC are the cause of immunoglobulin kappa light chain deficiency (IGKCD) [MIM:[http://omim.org/entry/614102 614102]]. IGKCD is a disease characterized by the complete absence of immunoglobulin kappa chains.<ref>PMID:3931219</ref> [[http://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[http://omim.org/entry/254500 254500]]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.
-	== Function ==
-
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 22:40, 22 December 2014

2014-12-22T22:40:24Z

←Older revision		Revision as of 22:40, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=1D5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D5I FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=1D5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D5I FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1axs\|1axs]], [[1d5b\|1d5b]], [[1d6v\|1d6v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1axs\|1axs]], [[1d5b\|1d5b]], [[1d6v\|1d6v]]</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=1d5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d5i RCSB], [http://www.ebi.ac.uk/pdbsum/1d5i 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=1d5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d5i RCSB], [http://www.ebi.ac.uk/pdbsum/1d5i PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/IGKC_HUMAN IGKC_HUMAN]] Defects in IGKC are the cause of immunoglobulin kappa light chain deficiency (IGKCD) [MIM:[http://omim.org/entry/614102 614102]]. IGKCD is a disease characterized by the complete absence of immunoglobulin kappa chains.<ref>PMID:3931219</ref> [[http://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[http://omim.org/entry/254500 254500]]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.		[[http://www.uniprot.org/uniprot/IGKC_HUMAN IGKC_HUMAN]] Defects in IGKC are the cause of immunoglobulin kappa light chain deficiency (IGKCD) [MIM:[http://omim.org/entry/614102 614102]]. IGKCD is a disease characterized by the complete absence of immunoglobulin kappa chains.<ref>PMID:3931219</ref> [[http://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[http://omim.org/entry/254500 254500]]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.
Line 38:		Line 38:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Hanson, M A.]]	+	[[Category: Hanson, M A]]
-	[[Category: Mundorff, E C.]]	+	[[Category: Mundorff, E C]]
-	[[Category: Schultz, P G.]]	+	[[Category: Schultz, P G]]
-	[[Category: Stevens, R C.]]	+	[[Category: Stevens, R C]]
	[[Category: Immune system]]		[[Category: Immune system]]

OCA at 16:20, 29 September 2014

2014-09-29T16:20:59Z

←Older revision		Revision as of 16:20, 29 September 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1d5i\| PDB=1d5i \| SCENE= }}~~	+	==UNLIGANDED GERMLINE PRECURSOR OF AN OXY-COPE CATALYTIC ANTIBODY==
-	===UNLIGANDED GERMLINE PRECURSOR OF AN OXY-COPE CATALYTIC ANTIBODY===	+	<StructureSection load='1d5i' size='340' side='right' caption='[[1d5i]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_10651626}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1d5i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=1D5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D5I FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1axs\|1axs]], [[1d5b\|1d5b]], [[1d6v\|1d6v]]</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=1d5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d5i RCSB], [http://www.ebi.ac.uk/pdbsum/1d5i PDBsum]</span></td></tr>
		+	<table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/IGKC_HUMAN IGKC_HUMAN]] Defects in IGKC are the cause of immunoglobulin kappa light chain deficiency (IGKCD) [MIM:[http://omim.org/entry/614102 614102]]. IGKCD is a disease characterized by the complete absence of immunoglobulin kappa chains.<ref>PMID:3931219</ref> [[http://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[http://omim.org/entry/254500 254500]]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.
		+	== Function ==

-	==~~Disease~~==	+	== Evolutionary Conservation ==
-	[[~~http~~://~~www~~.~~uniprot.org~~/~~uniprot~~/~~IGKC_HUMAN IGKC_HUMAN]] Defects in IGKC are the cause of immunoglobulin kappa light chain deficiency (IGKCD) [MIM:[http:~~//~~omim.org~~/~~entry~~/~~614102 614102]]~~. ~~IGKCD is a disease characterized by~~ the ~~complete absence of immunoglobulin kappa chains.~~<~~ref~~>~~PMID:3931219~~</~~ref~~> [[http://~~www~~.~~uniprot~~.~~org~~/~~uniprot/IGHG1_HUMAN IGHG1_HUMAN~~]] ~~Defects in IGHG1 are a cause~~ of ~~multiple myeloma (MM) [MIM:~~[http://~~omim~~.~~org~~/~~entry~~/~~254500 254500]~~]. ~~MM is a malignant tumor~~ of ~~plasma cells usually arising~~ in the ~~bone marrow~~ and ~~characterized by diffuse involvement~~ of the ~~skeletal system~~, ~~hyperglobulinemia, Bence~~-~~Jones proteinuria~~ and ~~anemia~~. ~~Complications~~ of ~~multiple myeloma are bone pain~~, ~~hypercalcemia, renal failure~~ and ~~spinal cord compression~~. The ~~aberrant antibodies that~~ are ~~produced lead~~ to ~~impaired humoral immunity~~ and ~~patients have a high prevalence~~ of ~~infection~~. ~~Amyloidosis may develop in some patients. Multiple myeloma is part~~ of ~~a spectrum~~ of ~~diseases ranging~~ from ~~monoclonal gammopathy~~ of ~~unknown significance (MGUS) to plasma cell leukemia~~. ~~Note=A chromosomal aberration involving IGHG1 is found~~ in ~~multiple myeloma~~. ~~Translocation t(11;14)(q13;q32) with~~ the ~~IgH locus~~. ~~Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16~~.~~3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4~~.	+	[[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/d5/1d5i_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 ==
		+	Antibody AZ-28 was generated against the chairlike transition-state analogue (TSA) 1 and catalyzes the oxy-Cope rearrangement of substrate 2 to product 3. The germline precursor to AZ-28 catalyzes the reaction with a 35-fold higher rate (k(cat)/k(uncat) = 163 000), despite a 40-fold lower binding affinity for TSA.1 (K(D) = 670 nM). To determine the structural basis for the differences in the binding and catalytic properties of the germline and affinity-matured antibodies, the X-ray crystal structures of the unliganded and TSA.1 complex of antibody AZ-28 have been determined at 2.8 and 2.6 A resolution, respectively; the structures of the unliganded and TSA.1 complex of the germline precursor to AZ-28 were both determined at 2. 0 A resolution. In the affinity-matured antibody.hapten complex the TSA is fixed in a catalytically unfavorable conformation by a combination of van der Waals and hydrogen-bonding interactions. The 2- and 5-phenyl substituents of TSA.1 are almost perpendicular to the cyclohexyl ring, leading to decreased orbital overlap and decreased stabilization of the putative transition state. The active site of the germline antibody appears to have an increased degree of flexibility-CDRH3 moves 4.9 A outward from the active site upon binding of TSA.1. We suggest that this conformational flexibility in the germline antibody, which results in a lower binding affinity for TSA.1, allows dynamic changes in the dihedral angle of the 2-phenyl substituent along the reaction coordinate. These conformational changes in turn lead to enhanced orbital overlap and increased catalytic rate. These studies suggest that protein and substrate dynamics play a key role in this antibody-catalyzed reaction.

-	~~==About this Structure==~~	+	Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement.,Mundorff EC, Hanson MA, Varvak A, Ulrich H, Schultz PG, Stevens RC Biochemistry. 2000 Feb 1;39(4):627-32. PMID:10651626<ref>PMID:10651626</ref>
-	~~[[1d5i]] is a 2 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens] 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=1D5I OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:010651626</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Monoclonal Antibody\|Monoclonal Antibody]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]

OCA at 04:20, 25 March 2013

2013-03-25T04:20:53Z

←Older revision		Revision as of 04:20, 25 March 2013
Line 1:		Line 1:
-	[[Image:1d5i.png\|left\|200px]]
-
	{{STRUCTURE_1d5i\| PDB=1d5i \| SCENE= }}		{{STRUCTURE_1d5i\| PDB=1d5i \| SCENE= }}
-
	===UNLIGANDED GERMLINE PRECURSOR OF AN OXY-COPE CATALYTIC ANTIBODY===		===UNLIGANDED GERMLINE PRECURSOR OF AN OXY-COPE CATALYTIC ANTIBODY===
		+	{{ABSTRACT_PUBMED_10651626}}

-	~~{{ABSTRACT_PUBMED_10651626}}~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/IGKC_HUMAN IGKC_HUMAN]] Defects in IGKC are the cause of immunoglobulin kappa light chain deficiency (IGKCD) [MIM:[http://omim.org/entry/614102 614102]]. IGKCD is a disease characterized by the complete absence of immunoglobulin kappa chains.<ref>PMID:3931219</ref> [[http://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[http://omim.org/entry/254500 254500]]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.

	==About this Structure==		==About this Structure==
-	[[1d5i]] 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=1D5I OCA].	+	[[1d5i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=1D5I OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:010651626</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010651626</ref><references group="xtra"/><references/>
		+	[[Category: Homo sapiens]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Hanson, M A.]]		[[Category: Hanson, M A.]]