6szx - Revision history

OCA at 12:51, 24 January 2024

2024-01-24T12:51:23Z

←Older revision		Revision as of 12:51, 24 January 2024
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	<StructureSection load='6szx' size='340' side='right'caption='[[6szx]], [[Resolution\|resolution]] 1.17Å' scene=''>		<StructureSection load='6szx' size='340' side='right'caption='[[6szx]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6szx]] 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=6SZX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6SZX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6szx]] 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=6SZX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SZX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M4K:6-[[cyclopropyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione'>M4K</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]] 1.17Å</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=6szx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szx OCA], [~~http~~://pdbe.org/6szx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6szx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6szx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6szx ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M4K:6-[[cyclopropyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione'>M4K</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'>[https://proteopedia.org/fgij/fg.htm?mol=6szx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szx OCA], [https://pdbe.org/6szx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6szx RCSB], [https://www.ebi.ac.uk/pdbsum/6szx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6szx 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

2020-04-01T09:43:37Z

←Older revision		Revision as of 09:43, 1 April 2020
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	<StructureSection load='6szx' size='340' side='right'caption='[[6szx]], [[Resolution\|resolution]] 1.17Å' scene=''>		<StructureSection load='6szx' size='340' side='right'caption='[[6szx]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6szx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SZX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6szx]] 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=6SZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SZX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M4K:6-[[cyclopropyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione'>M4K</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=M4K:6-[[cyclopropyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione'>M4K</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=6szx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szx OCA], [http://pdbe.org/6szx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6szx RCSB], [http://www.ebi.ac.uk/pdbsum/6szx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6szx 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=6szx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szx OCA], [http://pdbe.org/6szx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6szx RCSB], [http://www.ebi.ac.uk/pdbsum/6szx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6szx ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bedi, R K]]		[[Category: Bedi, R K]]

OCA at 06:51, 4 March 2020

2020-03-04T06:51:07Z

←Older revision		Revision as of 06:51, 4 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6szx is ~~ON HOLD~~	+	==Crystal structure of YTHDC1 with fragment 11 (DHU_DC1_128)==
		+	<StructureSection load='6szx' size='340' side='right'caption='[[6szx]], [[Resolution\|resolution]] 1.17Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6szx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SZX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M4K:6-[[cyclopropyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione'>M4K</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=6szx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szx OCA], [http://pdbe.org/6szx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6szx RCSB], [http://www.ebi.ac.uk/pdbsum/6szx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6szx 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 11 (DHU_DC1_128)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Sledz~~, P]]	+	<div class="pdbe-citations 6szx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bedi, R K]]
	[[Category: Caflisch, A]]		[[Category: Caflisch, A]]
-	[[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: Protected "6szx" [edit=sysop:move=sysop]

2019-10-10T03:47:01Z

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

←Older revision

Revision as of 03:47, 10 October 2019

OCA: New page: '''Unreleased structure''' The entry 6szx is ON HOLD Authors: Bedi, R.K., Huang, D., Sledz, P., Caflisch, A. Description: Crystal structure of YTHDC1 with fragment 11 (DHU_DC1_128) [[C...

2019-10-10T03:47:00Z

New page: '''Unreleased structure''' The entry 6szx is ON HOLD Authors: Bedi, R.K., Huang, D., Sledz, P., Caflisch, A. Description: Crystal structure of YTHDC1 with fragment 11 (DHU_DC1_128) [[C...

New page

'''Unreleased structure'''

The entry 6szx is ON HOLD

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

Description: Crystal structure of YTHDC1 with fragment 11 (DHU_DC1_128)
[[Category: Unreleased Structures]]
[[Category: Sledz, P]]
[[Category: Caflisch, A]]
[[Category: Bedi, R.K]]
[[Category: Huang, D]]