5x5x - Revision history

OCA at 07:54, 22 November 2023

2023-11-22T07:54:23Z

←Older revision		Revision as of 07:54, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5x5x' size='340' side='right'caption='[[5x5x]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5x5x' size='340' side='right'caption='[[5x5x]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X5X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5x]] 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=5X5X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X5X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.9Å</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=5x5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5x OCA], [~~http~~://pdbe.org/5x5x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x5x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x5x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5x ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=5x5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5x OCA], [https://pdbe.org/5x5x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x5x RCSB], [https://www.ebi.ac.uk/pdbsum/5x5x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5x ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Small peptides with less than 1000 in molecular weight are not considered amenable to sandwich immunoassays due to their difficulty of simultaneous recognition by two antibodies. As an alternative, we attempted noncompetitive detection of small peptides by open sandwich enzyme-linked immunosorbent assay (OS-ELISA) utilizing the antigen-induced enhancement of antibody VH/VL interaction. Taking fragments of human osteocalcin (BGP), a major non-collagen peptide produced in bone, as model peptides, OS immunoassay was performed using the cloned VH and VL cDNAs from two anti-BGP monoclonal antibodies either recognizing the N- or C-terminal fragment, respectively. When the clones were used for OS-ELISA with immobilized VL fragment and phage-displayed VH fragment, enhanced VH/VL interaction upon BGP addition was observed. Especially the clone for the C-terminal fragment showed a superior detection limit as well as a wider working range than those of competitive assay. The result was reproduced with purified VH-alkaline phosphatase and MBP-VL fusion proteins, where the latter was directly immobilized onto the microplate wells. The minimum detectable fragment was the hexamer including the C-terminus. This simple approach with a single monoclonal antibody with a short measurement time may prove a useful tool in immunodiagnostics as well as in proteomics research.
-
-	Noncompetitive detection of low molecular weight peptides by open sandwich immunoassay.,Lim SL, Ichinose H, Shinoda T, Ueda H Anal Chem. 2007 Aug 15;79(16):6193-200. doi: 10.1021/ac070653z. Epub 2007 Jul 18. PMID:17636882<ref>PMID:17636882</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5x5x" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]		*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arai, R]]	+	[[Category: Mus musculus]]
-	[[Category: Dong, J]]	+	[[Category: Arai R]]
-	[[Category: Komatsu, M]]	+	[[Category: Dong J]]
-	[[Category: Ueda, H]]	+	[[Category: Komatsu M]]
-	~~[[Category: Immune system]]~~	+	[[Category: Ueda H]]
-	~~[[Category: Immunoglobulin fold]]~~	+
-	~~[[Category: Osteocalcin~~]]	+

OCA at 07:27, 7 October 2020

2020-10-07T07:27:29Z

←Older revision		Revision as of 07:27, 7 October 2020
Line 1:		Line 1:

	==Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219==		==Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219==
-	<StructureSection load='5x5x' size='340' side='right' caption='[[5x5x]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5x5x' size='340' side='right'caption='[[5x5x]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5X OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X5X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X5X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=5x5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5x OCA], [http://pdbe.org/5x5x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5x RCSB], [http://www.ebi.ac.uk/pdbsum/5x5x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5x 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=5x5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5x OCA], [http://pdbe.org/5x5x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5x RCSB], [http://www.ebi.ac.uk/pdbsum/5x5x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5x ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 5x5x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x5x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Arai, R]]		[[Category: Arai, R]]
	[[Category: Dong, J]]		[[Category: Dong, J]]

OCA at 07:20, 22 February 2018

2018-02-22T07:20:07Z

←Older revision		Revision as of 07:20, 22 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x5x is ~~ON HOLD until Feb 18 2019~~	+	==Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219==
		+	<StructureSection load='5x5x' size='340' side='right' caption='[[5x5x]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x5x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X5X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=5x5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5x OCA], [http://pdbe.org/5x5x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5x RCSB], [http://www.ebi.ac.uk/pdbsum/5x5x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5x ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Small peptides with less than 1000 in molecular weight are not considered amenable to sandwich immunoassays due to their difficulty of simultaneous recognition by two antibodies. As an alternative, we attempted noncompetitive detection of small peptides by open sandwich enzyme-linked immunosorbent assay (OS-ELISA) utilizing the antigen-induced enhancement of antibody VH/VL interaction. Taking fragments of human osteocalcin (BGP), a major non-collagen peptide produced in bone, as model peptides, OS immunoassay was performed using the cloned VH and VL cDNAs from two anti-BGP monoclonal antibodies either recognizing the N- or C-terminal fragment, respectively. When the clones were used for OS-ELISA with immobilized VL fragment and phage-displayed VH fragment, enhanced VH/VL interaction upon BGP addition was observed. Especially the clone for the C-terminal fragment showed a superior detection limit as well as a wider working range than those of competitive assay. The result was reproduced with purified VH-alkaline phosphatase and MBP-VL fusion proteins, where the latter was directly immobilized onto the microplate wells. The minimum detectable fragment was the hexamer including the C-terminus. This simple approach with a single monoclonal antibody with a short measurement time may prove a useful tool in immunodiagnostics as well as in proteomics research.

-	~~Authors~~:	+	Noncompetitive detection of low molecular weight peptides by open sandwich immunoassay.,Lim SL, Ichinose H, Shinoda T, Ueda H Anal Chem. 2007 Aug 15;79(16):6193-200. doi: 10.1021/ac070653z. Epub 2007 Jul 18. PMID:17636882<ref>PMID:17636882</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5x5x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arai, R]]
		+	[[Category: Dong, J]]
		+	[[Category: Komatsu, M]]
		+	[[Category: Ueda, H]]
		+	[[Category: Immune system]]
		+	[[Category: Immunoglobulin fold]]
		+	[[Category: Osteocalcin]]

OCA at 20:13, 15 March 2017

2017-03-15T20:13:02Z

←Older revision		Revision as of 20:13, 15 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x5x is ON HOLD	+	The entry 5x5x is ON HOLD until Feb 18 2019

	Authors:		Authors:

OCA: Protected "5x5x" [edit=sysop:move=sysop]

2017-03-09T15:47:42Z

Protected "5x5x" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:47, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x5x is ON HOLD Authors: Description: Category: Unreleased Structures

2017-03-09T15:47:41Z

New page: '''Unreleased structure''' The entry 5x5x is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5x5x is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]