6fvc - Revision history

OCA at 10:46, 14 June 2023

OCA — Wed, 14 Jun 2023 10:46:29 GMT

←Older revision		Revision as of 10:46, 14 June 2023
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	==Protein environment affects the water-tryptophan binding mode. Molecular dynamics simulations of Engrailed homeodomain mutants==		==Protein environment affects the water-tryptophan binding mode. Molecular dynamics simulations of Engrailed homeodomain mutants==
-	<StructureSection load='6fvc' size='340' side='right'caption='[[6fvc~~]], [[NMR_Ensembles_of_Models \| 3 NMR models~~]]' scene=''>	+	<StructureSection load='6fvc' size='340' side='right'caption='[[6fvc]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6fvc]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Drome Drome~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FVC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6FVC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6fvc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FVC FirstGlance]. <br>
-	</td></tr>~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">en, CG9015 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>~~	+	</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=6fvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fvc OCA], [https://pdbe.org/6fvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fvc RCSB], [https://www.ebi.ac.uk/pdbsum/6fvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fvc 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=6fvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fvc OCA], [~~http~~://pdbe.org/6fvc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6fvc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6fvc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6fvc ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HMEN_DROME HMEN_DROME]] This protein specifies the body segmentation pattern. It is required for the development of the central nervous system. Transcriptional regulator that represses activated promoters. Wg signaling operates by inactivating the SGG repression of EN autoactivation.	+	[https://www.uniprot.org/uniprot/HMEN_DROME HMEN_DROME] This protein specifies the body segmentation pattern. It is required for the development of the central nervous system. Transcriptional regulator that represses activated promoters. Wg signaling operates by inactivating the SGG repression of EN autoactivation.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Water molecules can interact with aromatic moieties using either their O-H bonds or their lone-pairs of electrons. In proteins, water-pi interactions have been reported to occur with tryptophan and histidine residues, and dynamic exchange between O-Hpi hydrogen bonding and lone-pairpi interactions was suggested to take place, based on ab initio calculations. Here we used classical and QM/MM molecular dynamics simulations, complemented with an NMR study, to examine a specific water-indole interaction observed in the engrailed homeodomain and in its mutants. Our simulations indicate that the binding mode between water and indole can adapt to the potential created by the surrounding amino acids (and by the residues at the DNA surface in protein-DNA complexes), and support the model of dynamic switching between the O-Hpi hydrogen bonding and lone-pairpi binding modes.
		+
		+	Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants.,Spackova N, Trosanova Z, Sebesta F, Jansen S, Burda JV, Srb P, Zachrdla M, Zidek L, Kozelka J Phys Chem Chem Phys. 2018 May 9;20(18):12664-12677. doi: 10.1039/c7cp08623g. PMID:29696277<ref>PMID:29696277</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6fvc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jansen, S]]	+	[[Category: Jansen S]]
-	[[Category: Kozelka, J]]	+	[[Category: Kozelka J]]
-	[[Category: Srb, P]]	+	[[Category: Srb P]]
-	[[Category: Trosanova, Z]]	+	[[Category: Trosanova Z]]
-	[[Category: Zachrdla, M]]	+	[[Category: Zachrdla M]]
-	[[Category: Zidek, L]]	+	[[Category: Zidek L]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Engrailed homeodomain]]~~	+
-	~~[[Category: K52e mutation~~]]	+

OCA at 13:28, 10 May 2019

OCA — Fri, 10 May 2019 13:28:34 GMT

←Older revision		Revision as of 13:28, 10 May 2019
Line 3:		Line 3:
	<StructureSection load='6fvc' size='340' side='right'caption='[[6fvc]], [[NMR_Ensembles_of_Models \| 3 NMR models]]' scene=''>		<StructureSection load='6fvc' size='340' side='right'caption='[[6fvc]], [[NMR_Ensembles_of_Models \| 3 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6fvc]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FVC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6fvc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FVC FirstGlance]. <br>
-	</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=6fvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fvc OCA], [http://pdbe.org/6fvc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fvc RCSB], [http://www.ebi.ac.uk/pdbsum/6fvc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fvc ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">en, CG9015 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=6fvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fvc OCA], [http://pdbe.org/6fvc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fvc RCSB], [http://www.ebi.ac.uk/pdbsum/6fvc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fvc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 10:		Line 11:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Drome]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Jansen, S]]		[[Category: Jansen, S]]

OCA at 06:54, 3 April 2019

OCA — Wed, 03 Apr 2019 06:54:58 GMT

←Older revision		Revision as of 06:54, 3 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6fvc ~~is ON HOLD~~	+	==Protein environment affects the water-tryptophan binding mode. Molecular dynamics simulations of Engrailed homeodomain mutants==
-		+	<StructureSection load='6fvc' size='340' side='right'caption='[[6fvc]], [[NMR_Ensembles_of_Models \| 3 NMR models]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6fvc]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FVC FirstGlance]. <br>
-	~~Description~~:	+	</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=6fvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fvc OCA], [http://pdbe.org/6fvc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fvc RCSB], [http://www.ebi.ac.uk/pdbsum/6fvc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fvc ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HMEN_DROME HMEN_DROME]] This protein specifies the body segmentation pattern. It is required for the development of the central nervous system. Transcriptional regulator that represses activated promoters. Wg signaling operates by inactivating the SGG repression of EN autoactivation.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Jansen, S]]
		+	[[Category: Kozelka, J]]
		+	[[Category: Srb, P]]
		+	[[Category: Trosanova, Z]]
		+	[[Category: Zachrdla, M]]
		+	[[Category: Zidek, L]]
		+	[[Category: Dna]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Engrailed homeodomain]]
		+	[[Category: K52e mutation]]

OCA at 07:08, 13 February 2019

OCA — Wed, 13 Feb 2019 07:08:10 GMT

←Older revision		Revision as of 07:08, 13 February 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6fvc is ON HOLD ~~until sometime in the future~~	+	The entry 6fvc is ON HOLD

	Authors:		Authors:

OCA at 05:14, 14 March 2018

OCA — Wed, 14 Mar 2018 05:14:06 GMT

←Older revision		Revision as of 05:14, 14 March 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6fvc is ON HOLD	+	The entry 6fvc is ON HOLD until sometime in the future

	Authors:		Authors:

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

OCA — Thu, 08 Mar 2018 04:00:19 GMT

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

←Older revision

Revision as of 04:00, 8 March 2018

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

OCA — Thu, 08 Mar 2018 04:00:18 GMT

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

New page

'''Unreleased structure'''

The entry 6fvc is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]