6us9 - Revision history

OCA at 07:57, 11 October 2023

OCA — Wed, 11 Oct 2023 07:57:24 GMT

←Older revision		Revision as of 07:57, 11 October 2023
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	<StructureSection load='6us9' size='340' side='right'caption='[[6us9]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6us9' size='340' side='right'caption='[[6us9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6us9]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6US9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6US9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6us9]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Jinfang/132/2002(H3N2)) Influenza A virus (A/Jinfang/132/2002(H3N2))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6US9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6US9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=RIM:RIMANTADINE'>RIM</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]] 2Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=RIM:RIMANTADINE'>RIM</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=6us9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6us9 OCA], [https://pdbe.org/6us9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6us9 RCSB], [https://www.ebi.ac.uk/pdbsum/6us9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6us9 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=6us9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6us9 OCA], [https://pdbe.org/6us9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6us9 RCSB], [https://www.ebi.ac.uk/pdbsum/6us9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6us9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D5F6K1_9INFA D5F6K1_9INFA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6us9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6us9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ion channels 3D structures\|Ion channels 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: DeGrado~~, W F~~]]	+	[[Category: DeGrado WF]]
-	[[Category: Thomaston~~, J L]]~~	+	[[Category: Thomaston JL]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Proton channel]]~~	+
-	~~[[Category: Rimantadine~~]]	+

OCA at 07:55, 10 November 2021

OCA — Wed, 10 Nov 2021 07:55:29 GMT

←Older revision		Revision as of 07:55, 10 November 2021
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	==Influenza A M2 proton channel wild type TM domain bound to R-rimantadine==		==Influenza A M2 proton channel wild type TM domain bound to R-rimantadine==
-	<StructureSection load='6us9' size='340' side='right'caption='[[6us9]]' scene=''>	+	<StructureSection load='6us9' size='340' side='right'caption='[[6us9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6US9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6US9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6us9]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6US9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6US9 FirstGlance]. <br>
-	</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=6us9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6us9 OCA], [~~http~~://pdbe.org/6us9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6us9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6us9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6us9 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RIM:RIMANTADINE'>RIM</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</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=6us9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6us9 OCA], [https://pdbe.org/6us9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6us9 RCSB], [https://www.ebi.ac.uk/pdbsum/6us9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6us9 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The influenza A M2 wild-type (WT) proton channel is the target of the anti-influenza drug rimantadine. Rimantadine has two enantiomers, though most investigations into drug binding and inhibition have used a racemic mixture. Solid-state NMR experiments using the full length-M2 WT have shown significant spectral differences that were interpreted to indicate tighter binding for (R)- vs (S)-rimantadine. However, it was unclear if this correlates with a functional difference in drug binding and inhibition. Using X-ray crystallography, we have determined that both (R)- and (S)-rimantadine bind to the M2 WT pore with slight differences in the hydration of each enantiomer. However, this does not result in a difference in potency or binding kinetics, as shown by similar values for kon, koff, and Kd in electrophysiological assays and for EC50 values in cellular assays. We concluded that the slight differences in hydration for the (R)- and (S)-rimantadine enantiomers are not relevant to drug binding or channel inhibition. To further explore the effect of the hydration of the M2 pore on binding affinity, the water structure was evaluated by grand canonical ensemble molecular dynamics simulations as a function of the chemical potential of the water. Initially, the two layers of ordered water molecules between the bound drug and the channel's gating His37 residues mask the drug's chirality. As the chemical potential becomes more unfavorable, the drug translocates down to the lower water layer, and the interaction becomes more sensitive to chirality. These studies suggest the feasibility of displacing the upper water layer and specifically recognizing the lower water layers in novel drugs.
		+
		+	Rimantadine Binds to and Inhibits the Influenza A M2 Proton Channel without Enantiomeric Specificity.,Thomaston JL, Samways ML, Konstantinidi A, Ma C, Hu Y, Bruce Macdonald HE, Wang J, Essex JW, DeGrado WF, Kolocouris A Biochemistry. 2021 Aug 3. doi: 10.1021/acs.biochem.1c00437. PMID:34342217<ref>PMID:34342217</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6us9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: DeGrado WF]]	+	[[Category: DeGrado, W F]]
-	[[Category: Thomaston JL]]	+	[[Category: Thomaston, J L]]
		+	[[Category: Membrane protein]]
		+	[[Category: Proton channel]]
		+	[[Category: Rimantadine]]

OCA at 20:33, 28 October 2020

OCA — Wed, 28 Oct 2020 20:33:21 GMT

←Older revision		Revision as of 20:33, 28 October 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6us9 ~~is ON HOLD until Paper Publication~~	+	==Influenza A M2 proton channel wild type TM domain bound to R-rimantadine==
-		+	<StructureSection load='6us9' size='340' side='right'caption='[[6us9]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6US9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6US9 FirstGlance]. <br>
-	~~Description~~:	+	</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=6us9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6us9 OCA], [http://pdbe.org/6us9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6us9 RCSB], [http://www.ebi.ac.uk/pdbsum/6us9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6us9 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: DeGrado WF]]
		+	[[Category: Thomaston JL]]

OCA at 05:16, 19 February 2020

OCA — Wed, 19 Feb 2020 05:16:13 GMT

←Older revision		Revision as of 05:16, 19 February 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6us9 is ON HOLD	+	The entry 6us9 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6us9" [edit=sysop:move=sysop]

OCA — Wed, 06 Nov 2019 05:18:43 GMT

Protected "6us9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:18, 6 November 2019

OCA: New page: '''Unreleased structure''' The entry 6us9 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 06 Nov 2019 05:18:42 GMT

New page: '''Unreleased structure''' The entry 6us9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6us9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]