5jlw - Revision history

OCA at 18:58, 20 September 2023

OCA — Wed, 20 Sep 2023 18:58:07 GMT

←Older revision		Revision as of 18:58, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jlw' size='340' side='right'caption='[[5jlw]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='5jlw' size='340' side='right'caption='[[5jlw]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jlw]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JLW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JLW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jlw]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JLW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JLW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MPD:(4S)~~-2~~-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2.088Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class="sblockDat">[[5jlx\|5jlx]]</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=5jlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jlw OCA], [https://pdbe.org/5jlw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jlw RCSB], [https://www.ebi.ac.uk/pdbsum/5jlw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jlw ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Antp, CG1028 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])~~</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=5jlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jlw OCA], [~~http~~://pdbe.org/5jlw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jlw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jlw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jlw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ANTP_DROME ANTP_DROME]] Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis.	+	[https://www.uniprot.org/uniprot/ANTP_DROME ANTP_DROME] Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Iwahara, J]]	+	[[Category: Unidentified]]
-	[[Category: Nguyen, D]]	+	[[Category: Iwahara J]]
-	[[Category: White~~, M A~~]]	+	[[Category: Nguyen D]]
-	[[Category: Zandarashvili, L]]	+	[[Category: White MA]]
-	~~[[Category: Dna-binding protein]]~~	+	[[Category: Zandarashvili L]]
-	~~[[Category: Homeodomain]]~~	+
-	~~[[Category: Monothiolated dna]]~~	+
-	~~[[Category: Transcription regulator-dna complex]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 12:04, 25 December 2019

OCA — Wed, 25 Dec 2019 12:04:10 GMT

←Older revision		Revision as of 12:04, 25 December 2019
Line 1:		Line 1:

	==AntpHD with 15bp DNA duplex R-monothioated at Cytidine-8==		==AntpHD with 15bp DNA duplex R-monothioated at Cytidine-8==
-	<StructureSection load='5jlw' size='340' side='right' caption='[[5jlw]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='5jlw' size='340' side='right'caption='[[5jlw]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jlw]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JLW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JLW FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jlw]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JLW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JLW FirstGlance]. <br>
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Drome]]		[[Category: Drome]]
		+	[[Category: Large Structures]]
	[[Category: Iwahara, J]]		[[Category: Iwahara, J]]
	[[Category: Nguyen, D]]		[[Category: Nguyen, D]]

OCA at 12:55, 6 November 2017

OCA — Mon, 06 Nov 2017 12:55:17 GMT

←Older revision		Revision as of 12:55, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5jlw' size='340' side='right' caption='[[5jlw]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='5jlw' size='340' side='right' caption='[[5jlw]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jlw]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JLW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JLW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jlw]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JLW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JLW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jlx\|5jlx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jlx\|5jlx]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Antp, CG1028 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=5jlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jlw OCA], [http://pdbe.org/5jlw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jlw RCSB], [http://www.ebi.ac.uk/pdbsum/5jlw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jlw 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=5jlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jlw OCA], [http://pdbe.org/5jlw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jlw RCSB], [http://www.ebi.ac.uk/pdbsum/5jlw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jlw ProSAT]</span></td></tr>
	</table>		</table>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Drome]]
	[[Category: Iwahara, J]]		[[Category: Iwahara, J]]
	[[Category: Nguyen, D]]		[[Category: Nguyen, D]]

OCA at 11:58, 14 July 2016

OCA — Thu, 14 Jul 2016 11:58:43 GMT

←Older revision		Revision as of 11:58, 14 July 2016
Line 1:		Line 1:

-	==AntpHD with 15bp DNA duplex R-~~monothiolated~~ at Cytidine-8==	+	==AntpHD with 15bp DNA duplex R-monothioated at Cytidine-8==
	<StructureSection load='5jlw' size='340' side='right' caption='[[5jlw]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='5jlw' size='340' side='right' caption='[[5jlw]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 02:28, 13 July 2016

OCA — Wed, 13 Jul 2016 02:28:43 GMT

←Older revision		Revision as of 02:28, 13 July 2016
Line 7:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jlx\|5jlx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jlx\|5jlx]]</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=5jlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jlw OCA], [http://pdbe.org/5jlw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jlw RCSB], [http://www.ebi.ac.uk/pdbsum/5jlw PDBsum]</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=5jlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jlw OCA], [http://pdbe.org/5jlw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jlw RCSB], [http://www.ebi.ac.uk/pdbsum/5jlw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jlw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 23:10, 23 June 2016

OCA — Thu, 23 Jun 2016 23:10:50 GMT

←Older revision		Revision as of 23:10, 23 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jlw is ~~ON HOLD until Paper~~ Publication	+	==AntpHD with 15bp DNA duplex R-monothiolated at Cytidine-8==
		+	<StructureSection load='5jlw' size='340' side='right' caption='[[5jlw]], [[Resolution\|resolution]] 2.09Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jlw]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JLW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JLW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jlx\|5jlx]]</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=5jlw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jlw OCA], [http://pdbe.org/5jlw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jlw RCSB], [http://www.ebi.ac.uk/pdbsum/5jlw PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ANTP_DROME ANTP_DROME]] Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Oxygen-to-sulfur substitutions in DNA phosphate often enhance affinity for DNA-binding proteins. Our previous studies have suggested that this effect of sulfur substitution of both OP1 and OP2 atoms is due to an entropic gain associated with enhanced ion-pair dynamics. In this work, we studied stereospecific effects of single sulfur substitution of either the OP1 or OP2 atom in DNA phosphate at the Lys57 interaction site of the Antennapedia homeodomain-DNA complex. By crystallography, we obtained the structural information on the RP and SP diastereomers of the phosphoromonothioate and their interaction with Lys57. By fluorescence-based assays, we found significant affinity enhancement upon sulfur substitution of the OP2 atom. By NMR spectroscopy, we found significant mobilization of the Lys57 side-chain NH3+ group upon sulfur substitution of the OP2 atom. These data provide further mechanistic insight into the affinity enhancement by oxygen-to-sulfur substitution in DNA phosphate.

-	~~Authors~~:	+	Stereospecific effects of oxygen-to-sulfur substitution in DNA phosphate on ion-pair dynamics and protein-DNA affinity.,Nguyen D, Zandarashvili L, White MA, Iwahara J Chembiochem. 2016 Jun 7. doi: 10.1002/cbic.201600265. PMID:27271797<ref>PMID:27271797</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jlw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Iwahara, J]]
		+	[[Category: Nguyen, D]]
		+	[[Category: White, M A]]
		+	[[Category: Zandarashvili, L]]
		+	[[Category: Dna-binding protein]]
		+	[[Category: Homeodomain]]
		+	[[Category: Monothiolated dna]]
		+	[[Category: Transcription regulator-dna complex]]
		+	[[Category: Transcription-dna complex]]

OCA at 15:34, 15 May 2016

OCA — Sun, 15 May 2016 15:34:12 GMT

←Older revision		Revision as of 15:34, 15 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jlw is ON HOLD	+	The entry 5jlw is ON HOLD until Paper Publication

-	Authors: ~~White, M.A., Zandarashvili, L., Iwahara, J., Nguyen, D.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Zandarashvili, L]]
-	[[Category: White, M.A]]
-	[[Category: Iwahara, J]]
-	[[Category: Nguyen, D]]

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

OCA — Wed, 11 May 2016 02:16:54 GMT

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

←Older revision

Revision as of 02:16, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jlw is ON HOLD Authors: White, M.A., Zandarashvili, L., Iwahara, J., Nguyen, D. Description: Category: Unreleased Structures [[Category: Zand...

OCA — Wed, 11 May 2016 02:16:53 GMT

New page: '''Unreleased structure''' The entry 5jlw is ON HOLD Authors: White, M.A., Zandarashvili, L., Iwahara, J., Nguyen, D. Description: Category: Unreleased Structures [[Category: Zand...

New page

'''Unreleased structure'''

The entry 5jlw is ON HOLD

Authors: White, M.A., Zandarashvili, L., Iwahara, J., Nguyen, D.

Description:
[[Category: Unreleased Structures]]
[[Category: Zandarashvili, L]]
[[Category: White, M.A]]
[[Category: Iwahara, J]]
[[Category: Nguyen, D]]