5axe - Revision history

OCA at 15:50, 8 November 2023

2023-11-08T15:50:48Z

← Older revision		Revision as of 15:50, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5axe]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AXE FirstGlance]. <br>		<table><tr><td colspan='2'>[[5axe]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AXE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LSH:[(1R,5R,7R,8S)-7-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-8-OXIDANYL-3,3-BIS(OXIDANYLIDENE)-6-OXA-3$L^{6}-THIA-2-AZABICYCLO[3.2.1]OCTAN-5-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LSH</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 0.95Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LSH:[(1R,5R,7R,8S)-7-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-8-OXIDANYL-3,3-BIS(OXIDANYLIDENE)-6-OXA-3$L^{6}-THIA-2-AZABICYCLO[3.2.1]OCTAN-5-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LSH</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=5axe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axe OCA], [https://pdbe.org/5axe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5axe RCSB], [https://www.ebi.ac.uk/pdbsum/5axe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5axe 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=5axe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axe OCA], [https://pdbe.org/5axe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5axe RCSB], [https://www.ebi.ac.uk/pdbsum/5axe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5axe ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:29, 31 May 2023

2023-05-31T06:29:39Z

← Older revision		Revision as of 06:29, 31 May 2023
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	<StructureSection load='5axe' size='340' side='right'caption='[[5axe]], [[Resolution\|resolution]] 0.95Å' scene=''>		<StructureSection load='5axe' size='340' side='right'caption='[[5axe]], [[Resolution\|resolution]] 0.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5axe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AXE FirstGlance]. <br>		<table><tr><td colspan='2'>[[5axe]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AXE FirstGlance]. <br>
	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=LSH:[(1R,5R,7R,8S)-7-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-8-OXIDANYL-3,3-BIS(OXIDANYLIDENE)-6-OXA-3$L^{6}-THIA-2-AZABICYCLO[3.2.1]OCTAN-5-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LSH</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LSH:[(1R,5R,7R,8S)-7-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-8-OXIDANYL-3,3-BIS(OXIDANYLIDENE)-6-OXA-3$L^{6}-THIA-2-AZABICYCLO[3.2.1]OCTAN-5-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LSH</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5axf\|5axf]]~~</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=5axe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axe OCA], [https://pdbe.org/5axe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5axe RCSB], [https://www.ebi.ac.uk/pdbsum/5axe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5axe 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=5axe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axe OCA], [~~http~~://pdbe.org/5axe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5axe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5axe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5axe ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Aoyama, H]]		[[Category: Synthetic construct]]
	[[Category: Fujimura, Y]]		[[Category: Aoyama H]]
	[[Category: Hari, Y]]		[[Category: Fujimura Y]]
	[[Category: Kugimiya, A]]		[[Category: Hari Y]]
	[[Category: Mitsuoka, Y]]		[[Category: Kugimiya A]]
	[[Category: Noda, M]]		[[Category: Mitsuoka Y]]
	[[Category: Obika, S]]		[[Category: Noda M]]
	[[Category: Sawamura, M]]		[[Category: Obika S]]
	[[Category: Tahara, S]]		[[Category: Sawamura M]]
	[[Category: Wada, F]]		[[Category: Tahara S]]
	[[Category: Waki, R]]		[[Category: Wada F]]
	[[Category: Yamamoto, T]]		[[Category: Waki R]]
	~~[[Category: A-form dna]]~~		[[Category: Yamamoto T]]
	~~[[Category: Antisense]]~~
	~~[[Category: Dna]]~~
	~~[[Category: Sulfonamide-bridged nucleic acid~~]]

OCA at 06:54, 10 July 2019

2019-07-10T06:54:31Z

← Older revision		Revision as of 06:54, 10 July 2019
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	==Crystal Structure Analysis of DNA Duplexes containing sulfoamide-bridged nucleic acid (SuNA-NH)==		==Crystal Structure Analysis of DNA Duplexes containing sulfoamide-bridged nucleic acid (SuNA-NH)==
	<StructureSection load='5axe' size='340' side='right' caption='[[5axe]], [[Resolution\|resolution]] 0.95Å' scene=''>		<StructureSection load='5axe' size='340' side='right'caption='[[5axe]], [[Resolution\|resolution]] 0.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5axe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AXE FirstGlance]. <br>		<table><tr><td colspan='2'>[[5axe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AXE FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Aoyama, H]]		[[Category: Aoyama, H]]
	[[Category: Fujimura, Y]]		[[Category: Fujimura, Y]]

OCA at 15:12, 26 July 2016

2016-07-26T15:12:35Z

← Older revision		Revision as of 15:12, 26 July 2016
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	~~'''Unreleased structure'''~~

	~~The entry~~ 5axe is ~~ON HOLD until Paper~~ Publication		==Crystal Structure Analysis of DNA Duplexes containing sulfoamide-bridged nucleic acid (SuNA-NH)==
			<StructureSection load='5axe' size='340' side='right' caption='[[5axe]], [[Resolution\|resolution]] 0.95Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[5axe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AXE FirstGlance]. <br>
			</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LSH:[(1R,5R,7R,8S)-7-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-8-OXIDANYL-3,3-BIS(OXIDANYLIDENE)-6-OXA-3$L^{6}-THIA-2-AZABICYCLO[3.2.1]OCTAN-5-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LSH</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5axf\|5axf]]</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=5axe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axe OCA], [http://pdbe.org/5axe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5axe RCSB], [http://www.ebi.ac.uk/pdbsum/5axe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5axe ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			A sulfonamide-bridged nucleic acid without an N-substituent (SuNA[NH]) was successfully synthesized. A comparison of the SuNA[NMe]- and SuNA[NH]-modified oligonucleotides revealed that the duplex-forming abilities of the SuNA[NMe]-modified oligonucleotides with complementary DNA and RNA were higher than those of the SuNA[NH]-modified oligonucleotides. The crystal structures of DNA duplexes containing a SuNA[NR] revealed that the helical structures of the two duplexes and hydration patterns around the bridge moiety were different. These results provide insights into hydration patterns and rationale for the high RNA affinity of SuNA-modified oligonucleotides.

	~~Authors:~~ Mitsuoka, Y., Aoyama, H., Kugimiya, A., Fujimura, Y., Yamamoto, T., Waki, R., Wada, F., Tahara, S., Sawamura, M., Noda, M., Hari, Y., Obika, S.		Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure.,Mitsuoka Y, Aoyama H, Kugimiya A, Fujimura Y, Yamamoto T, Waki R, Wada F, Tahara S, Sawamura M, Noda M, Hari Y, Obika S Org Biomol Chem. 2016 Jul 6;14(27):6531-8. doi: 10.1039/c6ob01051b. PMID:27296230<ref>PMID:27296230</ref>

	~~Description: Crystal Structure Analysis~~ of ~~DNA Duplexes containing sulfoamide~~-~~bridged nucleic acid (SuNA~~-~~NH)~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[Category: Unreleased Structures]]~~		</div>
	~~[[Category: Yamamoto, T]]~~		<div class="pdbe-citations 5axe" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
	[[Category: Aoyama, H]]		[[Category: Aoyama, H]]
	[[Category: Fujimura, Y]]		[[Category: Fujimura, Y]]
	[[Category: ~~Sawamura~~, ~~M]]~~		[[Category: Hari, Y]]
	~~[[Category: Obika, S]]~~
	~~[[Category: Noda, M~~]]
	[[Category: Kugimiya, A]]		[[Category: Kugimiya, A]]
	[[Category: Mitsuoka, Y]]		[[Category: Mitsuoka, Y]]
			[[Category: Noda, M]]
			[[Category: Obika, S]]
			[[Category: Sawamura, M]]
	[[Category: Tahara, S]]		[[Category: Tahara, S]]
			[[Category: Wada, F]]
	[[Category: Waki, R]]		[[Category: Waki, R]]
	[[Category: ~~Wada~~, F]]		[[Category: Yamamoto, T]]
	[[Category: ~~Hari, Y~~]]		[[Category: A-form dna]]
			[[Category: Antisense]]
			[[Category: Dna]]
			[[Category: Sulfonamide-bridged nucleic acid]]

OCA at 09:58, 16 December 2015

2015-12-16T09:58:54Z

← Older revision		Revision as of 09:58, 16 December 2015
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yamamoto, T]]		[[Category: Yamamoto, T]]
			[[Category: Aoyama, H]]
	[[Category: Fujimura, Y]]		[[Category: Fujimura, Y]]
			[[Category: Sawamura, M]]
	[[Category: Obika, S]]		[[Category: Obika, S]]
	~~[[Category: Mitsuoka, Y]]~~
	~~[[Category: Wada, F]]~~
	~~[[Category: Aoyama, H]]~~
	~~[[Category: Sawamura, M]]~~
	[[Category: Noda, M]]		[[Category: Noda, M]]
	[[Category: Kugimiya, A]]		[[Category: Kugimiya, A]]
			[[Category: Mitsuoka, Y]]
	[[Category: Tahara, S]]		[[Category: Tahara, S]]
	[[Category: Waki, R]]		[[Category: Waki, R]]
			[[Category: Wada, F]]
	[[Category: Hari, Y]]		[[Category: Hari, Y]]

OCA at 12:24, 12 August 2015

2015-08-12T12:24:49Z

← Older revision		Revision as of 12:24, 12 August 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 5axe is ON HOLD		The entry 5axe is ON HOLD until Paper Publication

	Authors: Mitsuoka, Y., Aoyama, H., Kugimiya, A., Fujimura, Y., Yamamoto, T., Waki, R., Wada, F., Tahara, S., Sawamura, M., Noda, M., Hari, Y., Obika, S.		Authors: Mitsuoka, Y., Aoyama, H., Kugimiya, A., Fujimura, Y., Yamamoto, T., Waki, R., Wada, F., Tahara, S., Sawamura, M., Noda, M., Hari, Y., Obika, S.

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

2015-08-05T17:46:16Z

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

← Older revision	Revision as of 17:46, 5 August 2015
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5axe is ON HOLD Authors: Mitsuoka, Y., Aoyama, H., Kugimiya, A., Fujimura, Y., Yamamoto, T., Waki, R., Wada, F., Tahara, S., Sawamura, M., Noda, M.,...

2015-08-05T17:46:15Z

New page: '''Unreleased structure''' The entry 5axe is ON HOLD Authors: Mitsuoka, Y., Aoyama, H., Kugimiya, A., Fujimura, Y., Yamamoto, T., Waki, R., Wada, F., Tahara, S., Sawamura, M., Noda, M.,...

New page

'''Unreleased structure'''

The entry 5axe is ON HOLD

Authors: Mitsuoka, Y., Aoyama, H., Kugimiya, A., Fujimura, Y., Yamamoto, T., Waki, R., Wada, F., Tahara, S., Sawamura, M., Noda, M., Hari, Y., Obika, S.

Description: Crystal Structure Analysis of DNA Duplexes containing sulfoamide-bridged nucleic acid (SuNA-NH)
[[Category: Unreleased Structures]]
[[Category: Yamamoto, T]]
[[Category: Fujimura, Y]]
[[Category: Obika, S]]
[[Category: Mitsuoka, Y]]
[[Category: Wada, F]]
[[Category: Aoyama, H]]
[[Category: Sawamura, M]]
[[Category: Noda, M]]
[[Category: Kugimiya, A]]
[[Category: Tahara, S]]
[[Category: Waki, R]]
[[Category: Hari, Y]]