6szl - Revision history

OCA at 12:51, 24 January 2024

OCA — Wed, 24 Jan 2024 12:51:11 GMT

←Older revision		Revision as of 12:51, 24 January 2024
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	<StructureSection load='6szl' size='340' side='right'caption='[[6szl]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='6szl' size='340' side='right'caption='[[6szl]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6szl]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SZL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6SZL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6szl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SZL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SZL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3E:6-phenyl-1~{H}-pyrimidine-2,4-dione'>M3E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.45Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YTHDC1, KIAA1966, YT521 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M3E:6-phenyl-1~{H}-pyrimidine-2,4-dione'>M3E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6szl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szl OCA], [~~http~~://pdbe.org/6szl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6szl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6szl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6szl 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=6szl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szl OCA], [https://pdbe.org/6szl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6szl RCSB], [https://www.ebi.ac.uk/pdbsum/6szl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6szl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/YTDC1_HUMAN YTDC1_HUMAN]] RNA-binding protein that regulates alternative splice site selection.<ref>PMID:20167602</ref>	+	[https://www.uniprot.org/uniprot/YTDC1_HUMAN YTDC1_HUMAN] RNA-binding protein that regulates alternative splice site selection.<ref>PMID:20167602</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bedi~~, R K~~]]	+	[[Category: Bedi RK]]
-	[[Category: Caflisch, A]]	+	[[Category: Caflisch A]]
-	[[Category: Huang, D]]	+	[[Category: Huang D]]
-	[[Category: Sledz, P]]	+	[[Category: Sledz P]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Epitranscriptomic]]~~	+
-	~~[[Category: Fragment]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Ythdc1~~]]	+

OCA at 09:43, 1 April 2020

OCA — Wed, 01 Apr 2020 09:43:14 GMT

←Older revision		Revision as of 09:43, 1 April 2020
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	<StructureSection load='6szl' size='340' side='right'caption='[[6szl]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='6szl' size='340' side='right'caption='[[6szl]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6szl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SZL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6szl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SZL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3E:6-phenyl-1~{H}-pyrimidine-2,4-dione'>M3E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3E:6-phenyl-1~{H}-pyrimidine-2,4-dione'>M3E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YTHDC1, KIAA1966, YT521 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6szl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szl OCA], [http://pdbe.org/6szl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6szl RCSB], [http://www.ebi.ac.uk/pdbsum/6szl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6szl 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=6szl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szl OCA], [http://pdbe.org/6szl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6szl RCSB], [http://www.ebi.ac.uk/pdbsum/6szl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6szl ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bedi, R K]]		[[Category: Bedi, R K]]

OCA at 06:50, 4 March 2020

OCA — Wed, 04 Mar 2020 06:50:36 GMT

←Older revision		Revision as of 06:50, 4 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6szl is ~~ON HOLD~~ ~~until Oct 02 2021~~	+	==Crystal structure of YTHDC1 with fragment 7 (DHU_DC1_021)==
		+	<StructureSection load='6szl' size='340' side='right'caption='[[6szl]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6szl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SZL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3E:6-phenyl-1~{H}-pyrimidine-2,4-dione'>M3E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6szl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szl OCA], [http://pdbe.org/6szl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6szl RCSB], [http://www.ebi.ac.uk/pdbsum/6szl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6szl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YTDC1_HUMAN YTDC1_HUMAN]] RNA-binding protein that regulates alternative splice site selection.<ref>PMID:20167602</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report a crystallographic analysis of small-molecule ligands of the human YTHDC1 domain that recognizes N6-methylated adenine (m(6)A) in RNA. The 30 binders are fragments (molecular weight < 300 g mol(-1)) that represent 10 different chemotypes identified by virtual screening. Despite the structural disorder of the binding site loop (residues 429-439), most of the 30 fragments emulate the two main interactions of the -NHCH3 group of m(6)A. These interactions are the hydrogen bond to the backbone carbonyl of Ser378 and the van der Waals contacts with the tryptophan cage. Different chemical groups are involved in the conserved binding motifs. Some of the fragments show favorable ligand efficiency for YTHDC1 and selectivity against other m(6)A reader domains. The structural information is useful for the design of modulators of m(6)A recognition by YTHDC1.

-	~~Authors: Bedi, R.K~~., ~~Huang~~, D., ~~Sledz~~, P., ~~Caflisch~~, A.	+	Selectively Disrupting m(6)A-Dependent Protein-RNA Interactions with Fragments.,Bedi RK, Huang D, Wiedmer L, Li Y, Dolbois A, Wojdyla JA, Sharpe ME, Caflisch A, Sledz P ACS Chem Biol. 2020 Mar 2. doi: 10.1021/acschembio.9b00894. PMID:32101404<ref>PMID:32101404</ref>

-	~~Description: Crystal structure~~ of ~~YTHDC1 with fragment 7 (DHU_DC1_021)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6szl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bedi, R K]]
	[[Category: Caflisch, A]]		[[Category: Caflisch, A]]
-	[[Category: Sledz, P]]
-	[[Category: Bedi, R.K]]
	[[Category: Huang, D]]		[[Category: Huang, D]]
		+	[[Category: Sledz, P]]
		+	[[Category: Complex]]
		+	[[Category: Epitranscriptomic]]
		+	[[Category: Fragment]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Ythdc1]]

OCA at 05:14, 19 February 2020

OCA — Wed, 19 Feb 2020 05:14:27 GMT

←Older revision		Revision as of 05:14, 19 February 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6szl is ON HOLD	+	The entry 6szl is ON HOLD until Oct 02 2021

	Authors: Bedi, R.K., Huang, D., Sledz, P., Caflisch, A.		Authors: Bedi, R.K., Huang, D., Sledz, P., Caflisch, A.
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	Description: Crystal structure of YTHDC1 with fragment 7 (DHU_DC1_021)		Description: Crystal structure of YTHDC1 with fragment 7 (DHU_DC1_021)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Sledz, P]]
	[[Category: Caflisch, A]]		[[Category: Caflisch, A]]
		+	[[Category: Sledz, P]]
	[[Category: Bedi, R.K]]		[[Category: Bedi, R.K]]
	[[Category: Huang, D]]		[[Category: Huang, D]]

OCA: Protected "6szl" [edit=sysop:move=sysop]

OCA — Thu, 10 Oct 2019 03:46:06 GMT

Protected "6szl" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:46, 10 October 2019

OCA: New page: '''Unreleased structure''' The entry 6szl is ON HOLD Authors: Bedi, R.K., Huang, D., Sledz, P., Caflisch, A. Description: Crystal structure of YTHDC1 with fragment 7 (DHU_DC1_021) [[Ca...

OCA — Thu, 10 Oct 2019 03:46:05 GMT

New page: '''Unreleased structure''' The entry 6szl is ON HOLD Authors: Bedi, R.K., Huang, D., Sledz, P., Caflisch, A. Description: Crystal structure of YTHDC1 with fragment 7 (DHU_DC1_021) [[Ca...

New page

'''Unreleased structure'''

The entry 6szl is ON HOLD

Authors: Bedi, R.K., Huang, D., Sledz, P., Caflisch, A.

Description: Crystal structure of YTHDC1 with fragment 7 (DHU_DC1_021)
[[Category: Unreleased Structures]]
[[Category: Sledz, P]]
[[Category: Caflisch, A]]
[[Category: Bedi, R.K]]
[[Category: Huang, D]]