5zfx - Revision history

OCA at 08:53, 22 November 2023

OCA — Wed, 22 Nov 2023 08:53:41 GMT

←Older revision		Revision as of 08:53, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5zfx' size='340' side='right'caption='[[5zfx]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5zfx' size='340' side='right'caption='[[5zfx]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zfx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZFX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZFX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zfx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Opisthorchis_viverrini Opisthorchis viverrini]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZFX 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]] 1.751Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1]~~ </~~span~~></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5zfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zfx OCA], [~~http~~://pdbe.org/5zfx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zfx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zfx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zfx 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=5zfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zfx OCA], [https://pdbe.org/5zfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zfx RCSB], [https://www.ebi.ac.uk/pdbsum/5zfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zfx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A074Z863_9TREM A0A074Z863_9TREM]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5zfx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zfx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Triose phosphate isomerase 3D structures\|Triose phosphate isomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Triose-phosphate isomerase~~]]	+	[[Category: Opisthorchis viverrini]]
-	[[Category: Hwang~~, K Y~~]]	+	[[Category: Hwang KY]]
-	[[Category: Kim, S]]	+	[[Category: Kim S]]
-	[[Category: Kim~~, S E~~]]	+	[[Category: Kim SE]]
-	[[Category: Lee, H]]	+	[[Category: Lee H]]
-	[[Category: Lee~~, M R~~]]	+	[[Category: Lee MR]]
-	[[Category: Son, J]]	+	[[Category: Son J]]
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Tim-barrel]]~~	+
-	~~[[Category: Triosephosphate isomerase~~]]	+

OCA at 21:19, 28 October 2020

OCA — Wed, 28 Oct 2020 21:19:18 GMT

←Older revision		Revision as of 21:19, 28 October 2020
Line 1:		Line 1:

	==Crystal Structure of Triosephosphate isomerase from Opisthorchis viverrini==		==Crystal Structure of Triosephosphate isomerase from Opisthorchis viverrini==
-	<StructureSection load='5zfx' size='340' side='right' caption='[[5zfx]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5zfx' size='340' side='right'caption='[[5zfx]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zfx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZFX OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZFX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zfx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZFX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZFX 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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </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=5zfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zfx OCA], [http://pdbe.org/5zfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zfx RCSB], [http://www.ebi.ac.uk/pdbsum/5zfx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zfx 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=5zfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zfx OCA], [http://pdbe.org/5zfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zfx RCSB], [http://www.ebi.ac.uk/pdbsum/5zfx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zfx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Triose-phosphate isomerase]]		[[Category: Triose-phosphate isomerase]]
	[[Category: Hwang, K Y]]		[[Category: Hwang, K Y]]

OCA at 05:47, 24 October 2018

OCA — Wed, 24 Oct 2018 05:47:21 GMT

←Older revision		Revision as of 05:47, 24 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zfx is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Triosephosphate isomerase from Opisthorchis viverrini==
		+	<StructureSection load='5zfx' size='340' side='right' caption='[[5zfx]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zfx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZFX 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>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </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=5zfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zfx OCA], [http://pdbe.org/5zfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zfx RCSB], [http://www.ebi.ac.uk/pdbsum/5zfx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zfx ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Opisthorchis viverrini, a parasitic trematode, was recategorized as a group 1 biological carcinogen because it causes opisthorchiasis, which may result in cholangiocarcinoma. A new strategy for controlling opisthorchiasis is needed because of issues such as drug resistance and reinfection. Triosephosphate isomerase (TIM), a key enzyme in energy metabolism, is regarded as a potential drug target and vaccine candidate against various pathogens. Here, we determined the crystal structures of wild-type and 3 variants of TIMs from O. viverrini (OvTIM) at high resolution. The unique tripeptide of parasite trematodes, the SAD motif, was located on the surface of OvTIM and contributed to forming a 310-helix of the following loop in a sequence-independent manner. Through thermal stability and structural analyses of OvTIM variants, we found that the SAD motif induced local structural alterations of the surface and was involved in the overall stability of OvTIM in a complementary manner with another parasite-specific residue, N115. Comparison of the surface characteristics between OvTIM and Homo sapiens TIM (HsTIM) and structure-based epitope prediction suggested that the SAD motif functions as an epitope.

-	~~Authors:~~ Son, J., Kim, S., Kim~~, S.~~, Lee, H., Lee, M.R.~~, Hwang, K~~.Y.	+	Structural Analysis of an Epitope Candidate of Triosephosphate Isomerase in Opisthorchis viverrini.,Son J, Kim S, Kim SE, Lee H, Lee MR, Hwang KY Sci Rep. 2018 Oct 10;8(1):15075. doi: 10.1038/s41598-018-33479-8. PMID:30305716<ref>PMID:30305716</ref>

-	~~Description: Crystal Structure~~ of ~~Triosephosphate~~ isomerase ~~from Opisthorchis viverrini~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5zfx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Triose-phosphate isomerase]]
		+	[[Category: Hwang, K Y]]
	[[Category: Kim, S]]		[[Category: Kim, S]]
		+	[[Category: Kim, S E]]
	[[Category: Lee, H]]		[[Category: Lee, H]]
-	~~[[Category: Hwang, K.Y]]~~	+	[[Category: Lee, M R]]
-	[[Category: Lee, M.R]]	+
	[[Category: Son, J]]		[[Category: Son, J]]
		+	[[Category: Isomerase]]
		+	[[Category: Tim-barrel]]
		+	[[Category: Triosephosphate isomerase]]

OCA at 04:02, 18 April 2018

OCA — Wed, 18 Apr 2018 04:02:07 GMT

←Older revision		Revision as of 04:02, 18 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Son, J., Kim, S., Kim, S., Lee, H., Lee, M.R., Hwang, K.Y.		Authors: Son, J., Kim, S., Kim, S., Lee, H., Lee, M.R., Hwang, K.Y.

OCA at 05:08, 28 March 2018

OCA — Wed, 28 Mar 2018 05:08:10 GMT

←Older revision		Revision as of 05:08, 28 March 2018
Line 5:		Line 5:
	Authors: Son, J., Kim, S., Kim, S., Lee, H., Lee, M.R., Hwang, K.Y.		Authors: Son, J., Kim, S., Kim, S., Lee, H., Lee, M.R., Hwang, K.Y.

-	Description: Crystal Structure of Triosephosphate isomerase from ~~Clonorchis sinensis~~	+	Description: Crystal Structure of Triosephosphate isomerase from Opisthorchis viverrini
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kim, S]]		[[Category: Kim, S]]

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

OCA — Wed, 14 Mar 2018 05:01:26 GMT

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

←Older revision

Revision as of 05:01, 14 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zfx is ON HOLD Authors: Son, J., Kim, S., Kim, S., Lee, H., Lee, M.R., Hwang, K.Y. Description: Crystal Structure of Triosephosphate isomerase fro...

OCA — Wed, 14 Mar 2018 05:01:25 GMT

New page: '''Unreleased structure''' The entry 5zfx is ON HOLD Authors: Son, J., Kim, S., Kim, S., Lee, H., Lee, M.R., Hwang, K.Y. Description: Crystal Structure of Triosephosphate isomerase fro...

New page

'''Unreleased structure'''

The entry 5zfx is ON HOLD

Authors: Son, J., Kim, S., Kim, S., Lee, H., Lee, M.R., Hwang, K.Y.

Description: Crystal Structure of Triosephosphate isomerase from Clonorchis sinensis
[[Category: Unreleased Structures]]
[[Category: Kim, S]]
[[Category: Lee, H]]
[[Category: Hwang, K.Y]]
[[Category: Lee, M.R]]
[[Category: Son, J]]