7brx - Revision history

OCA at 15:28, 29 November 2023

OCA — Wed, 29 Nov 2023 15:28:39 GMT

←Older revision		Revision as of 15:28, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7brx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BRX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BRX FirstGlance]. <br>		<table><tr><td colspan='2'>[[7brx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BRX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BRX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=F5U:2-(5-methoxy-1H-indol-3-yl)ethanamine'>F5U</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]] 1.35Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:/~~/~~en.wikipedia.org/wiki/Trypsin Trypsin]~~, ~~with EC number [https~~:~~//www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~3~~.4.21.4 3.4.21.4]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=F5U:2-(5-methoxy-1H-indol-3-yl)ethanamine'>F5U</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=7brx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7brx OCA], [https://pdbe.org/7brx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7brx RCSB], [https://www.ebi.ac.uk/pdbsum/7brx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7brx 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=7brx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7brx OCA], [https://pdbe.org/7brx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7brx RCSB], [https://www.ebi.ac.uk/pdbsum/7brx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7brx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 28:
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Trypsin]]~~	+	[[Category: Funakubo T]]
-	[[Category: Funakubo, T]]	+	[[Category: Ishida A]]
-	[[Category: Ishida, A]]	+	[[Category: Ito S]]
-	[[Category: Ito, S]]	+	[[Category: Maeki M]]
-	[[Category: Maeki, M]]	+	[[Category: Takeda R]]
-	[[Category: Takeda, R]]	+	[[Category: Tani H]]
-	[[Category: Tani, H]]	+	[[Category: Tokeshi M]]
-	[[Category: Tokeshi, M]]	+	[[Category: Ueno G]]
-	[[Category: Ueno, G]]	+	[[Category: Yamamoto M]]
-	[[Category: Yamamoto, M]]	+
-	~~[[Category: Crystal sorting]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Microfluidic device]]~~	+
-	~~[[Category: Room temperature~~]]	+

OCA at 07:47, 25 June 2021

OCA — Fri, 25 Jun 2021 07:47:18 GMT

←Older revision		Revision as of 07:47, 25 June 2021
Line 1:		Line 1:

	==Bovine Pancreatic Trypsin with 5-Methoxytryptamine (Room Temperature)==		==Bovine Pancreatic Trypsin with 5-Methoxytryptamine (Room Temperature)==
-	<StructureSection load='7brx' size='340' side='right'caption='[[7brx]]' scene=''>	+	<StructureSection load='7brx' size='340' side='right'caption='[[7brx]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BRX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7BRX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7brx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BRX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BRX FirstGlance]. <br>
-	</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=7brx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7brx OCA], [~~http~~://pdbe.org/7brx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7brx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7brx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7brx ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=F5U:2-(5-methoxy-1H-indol-3-yl)ethanamine'>F5U</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </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=7brx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7brx OCA], [https://pdbe.org/7brx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7brx RCSB], [https://www.ebi.ac.uk/pdbsum/7brx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7brx ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Room-temperature (RT) protein crystallography provides significant information to elucidate protein function under physiological conditions. In particular, contrary to typical binding assays, X-ray crystal structure analysis of a protein-ligand complex can determine the three-dimensional (3D) configuration of its binding site. This allows the development of effective drugs by structure-based and fragment-based (FBDD) drug design. However, RT crystallography and RT crystallography-based protein-ligand complex analyses require the preparation and measurement of numerous crystals to avoid the X-ray radiation damage. Thus, for the application of RT crystallography to protein-ligand complex analysis, the simultaneous preparation of protein-ligand complex crystals and sequential X-ray diffraction measurement remain challenging. Here, we report an RT crystallography technique using a microfluidic protein crystal array device for protein-ligand complex structure analysis. We demonstrate the microfluidic sorting of protein crystals into microwells without any complicated procedures and apparatus, whereby the sorted protein crystals are fixed into microwells and sequentially measured to collect X-ray diffraction data. This is followed by automatic data processing to calculate the 3D protein structure. The microfluidic device allows the high-throughput preparation of the protein-ligand complex solely by the replacement of the microchannel content with the required ligand solution. We determined eight trypsin-ligand complex structures for the proof of concept experiment and found differences in the ligand coordination of the corresponding RT and conventional cryogenic structures. This methodology can be applied to easily obtain more natural structures. Moreover, drug development by FBDD could be more effective using the proposed methodology.
		+
		+	Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.,Maeki M, Ito S, Takeda R, Ueno G, Ishida A, Tani H, Yamamoto M, Tokeshi M Chem Sci. 2020 Aug 25;11(34):9072-9087. doi: 10.1039/d0sc02117b. PMID:34094189<ref>PMID:34094189</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7brx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Trypsin 3D structures\|Trypsin 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Funakubo T]]	+	[[Category: Trypsin]]
-	[[Category: Ishida A]]	+	[[Category: Funakubo, T]]
-	[[Category: Ito S]]	+	[[Category: Ishida, A]]
-	[[Category: Maeki M]]	+	[[Category: Ito, S]]
-	[[Category: Takeda R]]	+	[[Category: Maeki, M]]
-	[[Category: Tani H]]	+	[[Category: Takeda, R]]
-	[[Category: Tokeshi M]]	+	[[Category: Tani, H]]
-	[[Category: Ueno G]]	+	[[Category: Tokeshi, M]]
-	[[Category: Yamamoto M]]	+	[[Category: Ueno, G]]
		+	[[Category: Yamamoto, M]]
		+	[[Category: Crystal sorting]]
		+	[[Category: Hydrolase]]
		+	[[Category: Microfluidic device]]
		+	[[Category: Room temperature]]

OCA at 11:18, 26 August 2020

OCA — Wed, 26 Aug 2020 11:18:41 GMT

←Older revision		Revision as of 11:18, 26 August 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7brx ~~is ON HOLD~~	+	==Bovine Pancreatic Trypsin with 5-Methoxytryptamine (Room Temperature)==
-		+	<StructureSection load='7brx' size='340' side='right'caption='[[7brx]]' scene=''>
-	~~Authors~~: ~~Maeki, M~~.~~, Ito, S~~.~~, Takeda, R~~.~~, Funakubo, T~~., ~~Ueno, G~~., ~~Ishida, A~~., ~~Tani, H~~., ~~Yamamoto, M~~., ~~Tokeshi, M~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BRX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BRX FirstGlance]. <br>
-	~~Description: Bovine Pancreatic Trypsin with 5-Methoxytryptamine (Room Temperature)~~	+	</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=7brx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7brx OCA], [http://pdbe.org/7brx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7brx RCSB], [http://www.ebi.ac.uk/pdbsum/7brx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7brx ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Funakubo, T]]	+	__TOC__
-	[[Category: Ishida, A]]	+	</StructureSection>
-	[[Category: ~~Maeki, M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Yamamoto,~~ M]]	+	[[Category: Funakubo T]]
-	[[Category: Takeda, R]]	+	[[Category: Ishida A]]
-	[[Category: ~~Ito, S~~]]	+	[[Category: Ito S]]
-	[[Category: ~~Tani, H~~]]	+	[[Category: Maeki M]]
-	[[Category: ~~Tokeshi, M~~]]	+	[[Category: Takeda R]]
-	[[Category: ~~Ueno, G~~]]	+	[[Category: Tani H]]
		+	[[Category: Tokeshi M]]
		+	[[Category: Ueno G]]
		+	[[Category: Yamamoto M]]

OCA: Protected "7brx" [edit=sysop:move=sysop]

OCA — Wed, 08 Apr 2020 05:50:03 GMT

Protected "7brx" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:50, 8 April 2020

OCA: New page: '''Unreleased structure''' The entry 7brx is ON HOLD Authors: Maeki, M., Ito, S., Takeda, R., Funakubo, T., Ueno, G., Ishida, A., Tani, H., Yamamoto, M., Tokeshi, M. Description: Bovin...

OCA — Wed, 08 Apr 2020 05:50:01 GMT

New page: '''Unreleased structure''' The entry 7brx is ON HOLD Authors: Maeki, M., Ito, S., Takeda, R., Funakubo, T., Ueno, G., Ishida, A., Tani, H., Yamamoto, M., Tokeshi, M. Description: Bovin...

New page

'''Unreleased structure'''

The entry 7brx is ON HOLD

Authors: Maeki, M., Ito, S., Takeda, R., Funakubo, T., Ueno, G., Ishida, A., Tani, H., Yamamoto, M., Tokeshi, M.

Description: Bovine Pancreatic Trypsin with 5-Methoxytryptamine (Room Temperature)
[[Category: Unreleased Structures]]
[[Category: Funakubo, T]]
[[Category: Ishida, A]]
[[Category: Maeki, M]]
[[Category: Yamamoto, M]]
[[Category: Takeda, R]]
[[Category: Ito, S]]
[[Category: Tani, H]]
[[Category: Tokeshi, M]]
[[Category: Ueno, G]]