5ylu - Revision history

OCA at 08:33, 22 November 2023

2023-11-22T08:33:02Z

←Older revision		Revision as of 08:33, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of the gastric proton pump complexed with vonoprazan==		==Crystal structure of the gastric proton pump complexed with vonoprazan==
-	<StructureSection load='5ylu' size='340' side='right' caption='[[5ylu]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5ylu' size='340' side='right'caption='[[5ylu]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ylu]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pig Pig~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YLU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YLU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ylu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YLU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YLU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=HKT:1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine'>HKT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</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]] 2.7998896Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene>, <scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=HKT:1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine'>HKT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATP4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG]), ATP4B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</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=5ylu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ylu OCA], [https://pdbe.org/5ylu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ylu RCSB], [https://www.ebi.ac.uk/pdbsum/5ylu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ylu 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/Hydrogen/potassium-exchanging_ATPase Hydrogen/potassium-exchanging ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.10 3.6.3.10] </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=5ylu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ylu OCA], [~~http~~://pdbe.org/5ylu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ylu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ylu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ylu ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Disease ==
-	[[http://www.uniprot.org/uniprot/ATP4B_PIG ATP4B_PIG]] Note=Parietal cell autoantigen associated with autoimmune gastritis.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG]] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.	+	[https://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ylu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ylu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[ATPase 3D structures\|ATPase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hydrogen/potassium-exchanging ATPase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Pig~~]]	+	[[Category: Sus scrofa]]
-	[[Category: Abe, K]]	+	[[Category: Abe K]]
-	[[Category: Fujiyoshi, Y]]	+	[[Category: Fujiyoshi Y]]
-	[[Category: Irie, K]]	+	[[Category: Irie K]]
-	[[Category: Nakanishi, H]]	+	[[Category: Nakanishi H]]
-	~~[[Category: Gastric]]~~	+
-	~~[[Category: H+]]~~	+
-	~~[[Category: K+-atpase]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: P-type atpase]]~~	+
-	~~[[Category: Proton pump]]~~	+
-	~~[[Category: Transporter~~]]	+

OCA at 06:42, 18 April 2018

2018-04-18T06:42:00Z

←Older revision		Revision as of 06:42, 18 April 2018
Line 3:		Line 3:
	<StructureSection load='5ylu' size='340' side='right' caption='[[5ylu]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5ylu' size='340' side='right' caption='[[5ylu]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ylu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YLU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YLU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ylu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YLU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YLU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=HKT:1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine'>HKT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=HKT:1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine'>HKT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATP4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG]), ATP4B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogen/potassium-exchanging_ATPase Hydrogen/potassium-exchanging ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.10 3.6.3.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogen/potassium-exchanging_ATPase Hydrogen/potassium-exchanging ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.10 3.6.3.10] </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=5ylu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ylu OCA], [http://pdbe.org/5ylu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ylu RCSB], [http://www.ebi.ac.uk/pdbsum/5ylu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ylu 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=5ylu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ylu OCA], [http://pdbe.org/5ylu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ylu RCSB], [http://www.ebi.ac.uk/pdbsum/5ylu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ylu ProSAT]</span></td></tr>
Line 13:		Line 14:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG]] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.		[[http://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG]] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The gastric proton pump-the H(+), K(+)-ATPase-is a P-type ATPase responsible for acidifying the gastric juice down to pH 1. This corresponds to a million-fold proton gradient across the membrane of the parietal cell, the steepest known cation gradient of any mammalian tissue. The H(+), K(+)-ATPase is an important target for drugs that treat gastric acid-related diseases. Here we present crystal structures of the H(+), K(+)-ATPase in complex with two blockers, vonoprazan and SCH28080, in the luminal-open state, at 2.8 A resolution. The drugs have partially overlapping but clearly distinct binding modes in the middle of a conduit running from the gastric lumen to the cation-binding site. The crystal structures suggest that the tight configuration at the cation-binding site lowers the pK a value of Glu820 sufficiently to enable the release of a proton even into the pH 1 environment of the stomach.
		+
		+	Crystal structures of the gastric proton pump.,Abe K, Irie K, Nakanishi H, Suzuki H, Fujiyoshi Y Nature. 2018 Apr;556(7700):214-218. doi: 10.1038/s41586-018-0003-8. Epub 2018 Apr, 4. PMID:29618813<ref>PMID:29618813</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ylu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Hydrogen/potassium-exchanging ATPase]]		[[Category: Hydrogen/potassium-exchanging ATPase]]
		+	[[Category: Pig]]
	[[Category: Abe, K]]		[[Category: Abe, K]]
	[[Category: Fujiyoshi, Y]]		[[Category: Fujiyoshi, Y]]

OCA at 13:48, 11 April 2018

2018-04-11T13:48:33Z

←Older revision		Revision as of 13:48, 11 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ylu is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the gastric proton pump complexed with vonoprazan==
-		+	<StructureSection load='5ylu' size='340' side='right' caption='[[5ylu]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ylu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YLU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YLU FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=HKT:1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine'>HKT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogen/potassium-exchanging_ATPase Hydrogen/potassium-exchanging ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.10 3.6.3.10] </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=5ylu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ylu OCA], [http://pdbe.org/5ylu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ylu RCSB], [http://www.ebi.ac.uk/pdbsum/5ylu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ylu ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/ATP4B_PIG ATP4B_PIG]] Note=Parietal cell autoantigen associated with autoimmune gastritis.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG]] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hydrogen/potassium-exchanging ATPase]]
		+	[[Category: Abe, K]]
		+	[[Category: Fujiyoshi, Y]]
		+	[[Category: Irie, K]]
		+	[[Category: Nakanishi, H]]
		+	[[Category: Gastric]]
		+	[[Category: H+]]
		+	[[Category: K+-atpase]]
		+	[[Category: Membrane protein]]
		+	[[Category: P-type atpase]]
		+	[[Category: Proton pump]]
		+	[[Category: Transporter]]

OCA at 04:43, 1 November 2017

2017-11-01T04:43:49Z

←Older revision		Revision as of 04:43, 1 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2017-10-25T05:42:00Z

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

←Older revision

Revision as of 05:42, 25 October 2017

OCA: New page: '''Unreleased structure''' The entry 5ylu is ON HOLD Authors: Description: Category: Unreleased Structures

2017-10-25T05:41:59Z

New page: '''Unreleased structure''' The entry 5ylu is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ylu is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]