4h20 - Revision history

OCA at 14:58, 20 September 2023

2023-09-20T14:58:31Z

←Older revision		Revision as of 14:58, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4h20]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H20 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4h20]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H20 FirstGlance]. <br>
-	</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=4h20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h20 OCA], [https://pdbe.org/4h20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h20 RCSB], [https://www.ebi.ac.uk/pdbsum/4h20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h20 ProSAT]</span></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]] 1.9Å</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=4h20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h20 OCA], [https://pdbe.org/4h20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h20 RCSB], [https://www.ebi.ac.uk/pdbsum/4h20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h20 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:54, 3 November 2022

2022-11-03T07:54:39Z

←Older revision		Revision as of 07:54, 3 November 2022
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	<StructureSection load='4h20' size='340' side='right'caption='[[4h20]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4h20' size='340' side='right'caption='[[4h20]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h20]] 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=4H20 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4H20 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h20]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H20 FirstGlance]. <br>
-	</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=4h20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h20 OCA], [~~http~~://pdbe.org/4h20 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4h20 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4h20 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4h20 ProSAT]</span></td></tr>	+	</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=4h20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h20 OCA], [https://pdbe.org/4h20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h20 RCSB], [https://www.ebi.ac.uk/pdbsum/4h20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h20 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: LeCour~~, L F~~]]	+	[[Category: LeCour Jr LF]]
-	[[Category: Maresh, G]]	+	[[Category: Maresh G]]
-	[[Category: Pincus~~, S H~~]]	+	[[Category: Pincus SH]]
-	[[Category: Worthylake~~, D K~~]]	+	[[Category: Worthylake DK]]
-	[[Category: Zhao, Z]]	+	[[Category: Zhao Z]]
-	~~[[Category: Anti ricin antibody fab fragment]]~~	+
-	~~[[Category: Bloodstream]]~~	+
-	~~[[Category: Extracellular]]~~	+
-	~~[[Category: Ig]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Ricin a chain~~]]	+

OCA at 09:51, 5 February 2020

2020-02-05T09:51:40Z

←Older revision		Revision as of 09:51, 5 February 2020
Line 1:		Line 1:

	==Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18==		==Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18==
-	<StructureSection load='4h20' size='340' side='right' caption='[[4h20]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4h20' size='340' side='right'caption='[[4h20]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4h20]] 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=4H20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H20 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4h20]] 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=4H20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H20 FirstGlance]. <br>
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	==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: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: LeCour, L F]]		[[Category: LeCour, L F]]

OCA at 19:58, 15 December 2016

2016-12-15T19:58:36Z

←Older revision		Revision as of 19:58, 15 December 2016
Line 1:		Line 1:
		+
	==Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18==		==Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18==
	<StructureSection load='4h20' size='340' side='right' caption='[[4h20]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4h20' size='340' side='right' caption='[[4h20]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4h20]] 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=4H20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H20 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4h20]] 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=4H20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H20 FirstGlance]. <br>
-	</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=4h20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h20 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h20 RCSB], [http://www.ebi.ac.uk/pdbsum/4h20 PDBsum]</span></td></tr>	+	</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=4h20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h20 OCA], [http://pdbe.org/4h20 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h20 RCSB], [http://www.ebi.ac.uk/pdbsum/4h20 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h20 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4h20" style="background-color:#fffaf0;"></div>

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

OCA at 09:31, 10 December 2014

2014-12-10T09:31:40Z

←Older revision		Revision as of 09:31, 10 December 2014
Line 1:		Line 1:
-	[[~~Image~~:4h20.~~png\|left\|200px~~]]	+	==Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18==
		+	<StructureSection load='4h20' size='340' side='right' caption='[[4h20]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4h20]] 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=4H20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H20 FirstGlance]. <br>
		+	</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=4h20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h20 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h20 RCSB], [http://www.ebi.ac.uk/pdbsum/4h20 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Many antibody crystal structures have been solved. Structural modeling programs have been developed that utilize this information to predict 3-D structures of an antibody based upon its sequence. Because of the problem of self-reference, the accuracy and utility of these predictions can only be tested when a new structure has not yet been deposited in the Protein Data Bank. METHODS: We have solved the crystal structure of the Fab fragment of RAC18, a protective anti-ricin mAb, to 1.9 A resolution. We have also modeled the Fv structure of RAC18 using publicly available Ab modeling tools Prediction of Immunoglobulin Structures (PIGS), RosettaAntibody, and Web Antibody Modeling (WAM). The model structures underwent energy minimization. We compared results to the crystal structure on the basis of root-mean-square deviation (RMSD), template modeling score (TM-score), Z-score, and MolProbity analysis. FINDINGS: The crystal structure showed a pocket formed mainly by AA residues in each of the heavy chain complementarity determining regions (CDRs). There were differences between the crystal structure and structures predicted by the modeling tools, particularly in the CDRs. There were also differences among the predicted models, although the differences were small and within experimental error. No one modeling program was clearly superior to the others. In some cases, choosing structures based only on sequence homology to the crystallized Ab yielded RMSDs comparable to the models. CONCLUSIONS: Molecular modeling programs accurately predict the structure of most regions of antibody variable domains of RAC18. The hypervariable CDRs proved most difficult to model, particularly H chain CDR3. Because CDR3 is most often involved in contact with antigen, this defect must be considered when using models to identify potential contacts between antibody and antigen. Because this study represents only a single case, the results cannot be generalized. Rather they highlight the utility and limitations of modeling programs.

-	~~{{STRUCTURE_4h20\| PDB=4h20 \| SCENE= }}~~	+	Crystal structure and computational modeling of the fab fragment from a protective anti-ricin monoclonal antibody.,Zhao Z, Worthylake D, Lecour L Jr, Maresh GA, Pincus SH PLoS One. 2012;7(12):e52613. doi: 10.1371/journal.pone.0052613. Epub 2012 Dec 19. PMID:23285112<ref>PMID:23285112</ref>

-	~~===Crystal Structure and Computational Modeling~~ of the ~~Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_23285112}}~~	+	==See Also==
-		+	*[[Monoclonal Antibody\|Monoclonal Antibody]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~4h20~~]] ~~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=4H20 OCA].~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: LeCour, L F.]]	+	[[Category: LeCour, L F]]
-	[[Category: Maresh, G.]]	+	[[Category: Maresh, G]]
-	[[Category: Pincus, S H.]]	+	[[Category: Pincus, S H]]
-	[[Category: Worthylake, D K.]]	+	[[Category: Worthylake, D K]]
-	[[Category: Zhao, Z.]]	+	[[Category: Zhao, Z]]
	[[Category: Anti ricin antibody fab fragment]]		[[Category: Anti ricin antibody fab fragment]]
	[[Category: Bloodstream]]		[[Category: Bloodstream]]

OCA at 08:52, 16 January 2013

2013-01-16T08:52:35Z

←Older revision		Revision as of 08:52, 16 January 2013
Line 1:		Line 1:
-	[[Image:4h20.~~jpg~~\|left\|200px]]	+	[[Image:4h20.png\|left\|200px]]

	{{STRUCTURE_4h20\| PDB=4h20 \| SCENE= }}		{{STRUCTURE_4h20\| PDB=4h20 \| SCENE= }}
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	===Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18===		===Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18===

		+	{{ABSTRACT_PUBMED_23285112}}

	==About this Structure==		==About this Structure==

OCA at 07:29, 10 October 2012

2012-10-10T07:29:56Z

←Older revision		Revision as of 07:29, 10 October 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4h20.jpg\|left\|200px]]

-	~~The entry~~ 4h20 ~~is ON HOLD~~	+	{{STRUCTURE_4h20\| PDB=4h20 \| SCENE= }}

-	~~Authors: Zhao, Z., Worthylake, D.K., LeCour Jr., L.F., Maresh, G., Pincus, S.H.~~	+	===Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18===

-	~~Description: Crystal~~ Structure ~~and Computational Modeling of the Fab Fragment~~ from ~~the Protective anti~~-Ricin ~~Monoclonal Antibody RAC18~~	+
		+	==About this Structure==
		+	[[4h20]] 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=4H20 OCA].
		+	[[Category: Mus musculus]]
		+	[[Category: LeCour, L F.]]
		+	[[Category: Maresh, G.]]
		+	[[Category: Pincus, S H.]]
		+	[[Category: Worthylake, D K.]]
		+	[[Category: Zhao, Z.]]
		+	[[Category: Anti ricin antibody fab fragment]]
		+	[[Category: Bloodstream]]
		+	[[Category: Extracellular]]
		+	[[Category: Ig]]
		+	[[Category: Immune system]]
		+	[[Category: Ricin a chain]]

OCA at 20:10, 26 September 2012

2012-09-26T20:10:51Z

←Older revision		Revision as of 20:10, 26 September 2012
Line 3:		Line 3:
	The entry 4h20 is ON HOLD		The entry 4h20 is ON HOLD

-	Authors: Zhao, Z., Worthylake, D.K., LeCour Jr., L. F., Maresh, G., Pincus, S. H.	+	Authors: Zhao, Z., Worthylake, D.K., LeCour Jr., L.F., Maresh, G., Pincus, S.H.

	Description: Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18		Description: Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18

OCA: Protected "4h20" [edit=sysop:move=sysop]

2012-09-19T06:58:02Z

Protected "4h20" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:58, 19 September 2012

OCA: New page: '''Unreleased structure''' The entry 4h20 is ON HOLD Authors: Zhao, Z., Worthylake, D.K., LeCour Jr., L. F., Maresh, G., Pincus, S. H. Description: Crystal Structure and Computational ...

2012-09-19T06:58:01Z

New page: '''Unreleased structure''' The entry 4h20 is ON HOLD Authors: Zhao, Z., Worthylake, D.K., LeCour Jr., L. F., Maresh, G., Pincus, S. H. Description: Crystal Structure and Computational ...

New page

'''Unreleased structure'''

The entry 4h20 is ON HOLD

Authors: Zhao, Z., Worthylake, D.K., LeCour Jr., L. F., Maresh, G., Pincus, S. H.

Description: Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18