5l7x - Revision history

OCA at 16:10, 4 October 2023

OCA — Wed, 04 Oct 2023 16:10:40 GMT

←Older revision		Revision as of 16:10, 4 October 2023
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	<StructureSection load='5l7x' size='340' side='right'caption='[[5l7x]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='5l7x' size='340' side='right'caption='[[5l7x]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l7x]] 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=5L7X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5L7X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l7x]] 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=5L7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5L7X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.86Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5l7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l7x OCA], [~~http~~://pdbe.org/5l7x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5l7x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5l7x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5l7x ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=5l7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l7x OCA], [https://pdbe.org/5l7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5l7x RCSB], [https://www.ebi.ac.uk/pdbsum/5l7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5l7x 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: Naschberger, A]]	+	[[Category: Naschberger A]]
-	[[Category: Rupp, B]]	+	[[Category: Rupp B]]
-	~~[[Category: Afamin]]~~	+
-	~~[[Category: Antibody fragment]]~~	+
-	~~[[Category: Fab]]~~	+
-	~~[[Category: Glycosilated]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 07:00, 5 August 2020

OCA — Wed, 05 Aug 2020 07:00:25 GMT

←Older revision		Revision as of 07:00, 5 August 2020
Line 1:		Line 1:

	==Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form II==		==Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form II==
-	<StructureSection load='5l7x' size='340' side='right' caption='[[5l7x]], [[Resolution\|resolution]] 1.86Å' scene=''>	+	<StructureSection load='5l7x' size='340' side='right'caption='[[5l7x]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l7x]] 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=5L7X OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5L7X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l7x]] 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=5L7X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5L7X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></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=5l7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l7x OCA], [http://pdbe.org/5l7x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l7x RCSB], [http://www.ebi.ac.uk/pdbsum/5l7x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l7x ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5l7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l7x OCA], [http://pdbe.org/5l7x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l7x RCSB], [http://www.ebi.ac.uk/pdbsum/5l7x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l7x ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5l7x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5l7x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Sandbox 20009\|Sandbox 20009]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Naschberger, A]]		[[Category: Naschberger, A]]

OCA at 14:56, 22 December 2016

OCA — Thu, 22 Dec 2016 14:56:58 GMT

←Older revision		Revision as of 14:56, 22 December 2016
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	<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=5l7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l7x OCA], [http://pdbe.org/5l7x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l7x RCSB], [http://www.ebi.ac.uk/pdbsum/5l7x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l7x ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5l7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l7x OCA], [http://pdbe.org/5l7x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l7x RCSB], [http://www.ebi.ac.uk/pdbsum/5l7x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l7x ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The monoclonal antibody N14 is used as a detection antibody in ELISA kits for the human glycoprotein afamin, a member of the albumin family, which has recently gained interest in the capture and stabilization of Wnt signalling proteins, and for its role in metabolic syndrome and papillary thyroid carcinoma. As a rare occurrence, the N14 Fab is N-glycosylated at Asn26L at the onset of the VL1 antigen-binding loop, with the alpha-1-6 core fucosylated complex glycan facing out of the L1 complementarity-determining region. The crystal structures of two non-apparent (pseudo) isomorphous crystals of the N14 Fab were analyzed, which differ significantly in the elbow angles, thereby cautioning against the overinterpretation of domain movements upon antigen binding. In addition, the map quality at 1.9 A resolution was sufficient to crystallographically re-sequence the variable VL and VH domains and to detect discrepancies in the hybridoma-derived sequence. Finally, a conservatively refined parsimonious model is presented and its statistics are compared with those from a less conservatively built model that has been modelled more enthusiastically. Improvements to the PDB validation reports affecting ligands, clashscore and buried surface calculations are suggested.
		+
		+	The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling.,Naschberger A, Furnrohr BG, Lenac Rovis T, Malic S, Scheffzek K, Dieplinger H, Rupp B Acta Crystallogr D Struct Biol. 2016 Dec 1;72(Pt 12):1267-1280. Epub 2016 Nov 29. PMID:27917827<ref>PMID:27917827</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5l7x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:51, 14 July 2016

OCA — Thu, 14 Jul 2016 11:51:04 GMT

←Older revision		Revision as of 11:51, 14 July 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5l7x is ~~ON HOLD~~	+	==Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form II==
-		+	<StructureSection load='5l7x' size='340' side='right' caption='[[5l7x]], [[Resolution\|resolution]] 1.86Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5l7x]] 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=5L7X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5L7X FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5l7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l7x OCA], [http://pdbe.org/5l7x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l7x RCSB], [http://www.ebi.ac.uk/pdbsum/5l7x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l7x ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Mus musculus]]
		+	[[Category: Naschberger, A]]
		+	[[Category: Rupp, B]]
		+	[[Category: Afamin]]
		+	[[Category: Antibody fragment]]
		+	[[Category: Fab]]
		+	[[Category: Glycosilated]]
		+	[[Category: Immune system]]

OCA at 00:48, 13 July 2016

OCA — Wed, 13 Jul 2016 00:48:22 GMT

←Older revision		Revision as of 00:48, 13 July 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5l7x is ON HOLD ~~until Paper Publication~~	+	The entry 5l7x is ON HOLD

	Authors:		Authors:

OCA: Protected "5l7x" [edit=sysop:move=sysop]

OCA — Mon, 20 Jun 2016 14:00:44 GMT

Protected "5l7x" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:00, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5l7x is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Mon, 20 Jun 2016 14:00:43 GMT

New page: '''Unreleased structure''' The entry 5l7x is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5l7x is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]