5hru - Revision history

OCA at 10:52, 16 August 2023

OCA — Wed, 16 Aug 2023 10:52:08 GMT

←Older revision		Revision as of 10:52, 16 August 2023
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	<StructureSection load='5hru' size='340' side='right'caption='[[5hru]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='5hru' size='340' side='right'caption='[[5hru]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hru]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Haemamoeba_vivax Haemamoeba~~ vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HRU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HRU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hru]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Phylica_emirnensis Phylica emirnensis] and [https://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HRU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.71Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hs4\|5hs4]]~~, [[~~5hto~~\|~~5hto~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>LDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~5855 Haemamoeba vivax])</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=5hru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hru OCA], [https://pdbe.org/5hru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hru RCSB], [https://www.ebi.ac.uk/pdbsum/5hru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hru ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27]~~ </~~span~~></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=5hru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hru OCA], [~~http~~://pdbe.org/5hru PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hru RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hru PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hru ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q4PRK9_PLAVI Q4PRK9_PLAVI]
	<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: Haemamoeba vivax]]
-	[[Category: L-lactate dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ban, C~~]]	+	[[Category: Phylica emirnensis]]
-	[[Category: ~~Choi, S J~~]]	+	[[Category: Plasmodium vivax]]
-	[[Category: ~~Dna aptamer~~]]	+	[[Category: Ban C]]
-	[[Category: ~~Dna structural element]]~~	+	[[Category: Choi SJ]]
-	~~[[Category: Malaria]]~~	+
-	~~[[Category: Oxidoreductase-dna complex]]~~	+
-	~~[[Category: Plasmodium ldh~~]]	+

OCA at 08:29, 27 May 2020

OCA — Wed, 27 May 2020 08:29:42 GMT

←Older revision		Revision as of 08:29, 27 May 2020
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	==Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1==		==Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1==
-	<StructureSection load='5hru' size='340' side='right' caption='[[5hru]], [[Resolution\|resolution]] 1.71Å' scene=''>	+	<StructureSection load='5hru' size='340' side='right'caption='[[5hru]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hru]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HRU OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HRU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hru]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemamoeba_vivax Haemamoeba vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HRU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HRU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hs4\|5hs4]], [[5hto\|5hto]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hs4\|5hs4]], [[5hto\|5hto]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 Haemamoeba vivax])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </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=5hru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hru OCA], [http://pdbe.org/5hru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hru RCSB], [http://www.ebi.ac.uk/pdbsum/5hru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hru ProSAT]</span></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=5hru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hru OCA], [http://pdbe.org/5hru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hru RCSB], [http://www.ebi.ac.uk/pdbsum/5hru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hru ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5hru" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5hru" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lactate dehydrogenase 3D structures\|Lactate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Haemamoeba vivax]]
	[[Category: L-lactate dehydrogenase]]		[[Category: L-lactate dehydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Ban, C]]		[[Category: Ban, C]]
	[[Category: Choi, S J]]		[[Category: Choi, S J]]

OCA at 15:02, 22 December 2016

OCA — Thu, 22 Dec 2016 15:02:15 GMT

←Older revision		Revision as of 15:02, 22 December 2016
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	<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=5hru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hru OCA], [http://pdbe.org/5hru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hru RCSB], [http://www.ebi.ac.uk/pdbsum/5hru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hru 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=5hru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hru OCA], [http://pdbe.org/5hru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hru RCSB], [http://www.ebi.ac.uk/pdbsum/5hru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hru ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Structural elements are key elements for understanding single-stranded nucleic acid folding. Although various RNA structural elements have been documented, structural elements of single-stranded DNA (ssDNA) have rarely been reported. Herein, we determined a crystal structure of PvLDH in complex with a DNA aptamer called pL1. This aptamer folds into a hairpin-bulge contact by adopting three novel structural elements, viz, DNA T-loop-like motif, base-phosphate zipper, and DNA G.G metal ion zipper. Moreover, the pL1:PvLDH complex shows unique properties compared with other protein:nucleic acid complexes. Generally, extensive intermolecular hydrogen bonds occur between unpaired nucleotides and proteins for specific recognitions. Although most protein-interacting nucleotides of pL1 are unpaired nucleotides, pL1 recognizes PvLDH by predominant shape complementarity with many bridging water molecules owing to the combination of three novel structural elements making protein-binding unpaired nucleotides stable. Moreover, the additional set of Plasmodium LDH residues which were shown to form extensive hydrogen bonds with unpaired nucleotides of 2008s does not participate in the recognition of pL1. Superimposition of the pL1:PvLDH complex with hLDH reveals steric clashes between pL1 and hLDH in contrast with no steric clashes between 2008s and hLDH. Therefore, specific protein recognition mode of pL1 is totally different from that of 2008s.
		+
		+	Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition.,Choi SJ, Ban C Sci Rep. 2016 Oct 11;6:34998. doi: 10.1038/srep34998. PMID:27725738<ref>PMID:27725738</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5hru" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 00:58, 20 October 2016

OCA — Thu, 20 Oct 2016 00:58:33 GMT

←Older revision		Revision as of 00:58, 20 October 2016
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-	'''Unreleased structure'''

-	~~The entry 5hru is ON HOLD until Paper Publication~~	+	==Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1==
-		+	<StructureSection load='5hru' size='340' side='right' caption='[[5hru]], [[Resolution\|resolution]] 1.71Å' scene=''>
-	~~Authors: Choi, S.J., Ban, C.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5hru]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HRU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HRU FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hs4\|5hs4]], [[5hto\|5hto]]</td></tr>
-	[[~~Category~~: ~~Choi~~, S.J]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </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=5hru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hru OCA], [http://pdbe.org/5hru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hru RCSB], [http://www.ebi.ac.uk/pdbsum/5hru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hru ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: L-lactate dehydrogenase]]
	[[Category: Ban, C]]		[[Category: Ban, C]]
		+	[[Category: Choi, S J]]
		+	[[Category: Dna aptamer]]
		+	[[Category: Dna structural element]]
		+	[[Category: Malaria]]
		+	[[Category: Oxidoreductase-dna complex]]
		+	[[Category: Plasmodium ldh]]

OCA at 12:57, 2 March 2016

OCA — Wed, 02 Mar 2016 12:57:14 GMT

←Older revision		Revision as of 12:57, 2 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Choi, S.J., Ban, C.		Authors: Choi, S.J., Ban, C.

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

OCA — Wed, 03 Feb 2016 14:14:08 GMT

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

←Older revision

Revision as of 14:14, 3 February 2016

OCA: New page: '''Unreleased structure''' The entry 5hru is ON HOLD Authors: Choi, S.J., Ban, C. Description: Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1 [[Cate...

OCA — Wed, 03 Feb 2016 14:14:07 GMT

New page: '''Unreleased structure''' The entry 5hru is ON HOLD Authors: Choi, S.J., Ban, C. Description: Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1 [[Cate...

New page

'''Unreleased structure'''

The entry 5hru is ON HOLD

Authors: Choi, S.J., Ban, C.

Description: Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1
[[Category: Unreleased Structures]]
[[Category: Choi, S.J]]
[[Category: Ban, C]]