3qyo - Revision history

OCA at 10:50, 21 February 2024

OCA — Wed, 21 Feb 2024 10:50:54 GMT

←Older revision		Revision as of 10:50, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3qyo' size='340' side='right'caption='[[3qyo]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='3qyo' size='340' side='right'caption='[[3qyo]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qyo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Escherichia_coli_k~~-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QYO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qyo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QYO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO~~-~~NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>~~, ~~<scene name='pdbligand=Q24:QUINAZOLINE-~~2~~,4-DIAMINE'>Q24</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]] 2.09Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3qyl\|3qyl]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=Q24:QUINAZOLINE-2,4-DIAMINE'>Q24</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase]~~, ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3]~~ </~~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=3qyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyo OCA], [https://pdbe.org/3qyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qyo RCSB], [https://www.ebi.ac.uk/pdbsum/3qyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyo 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=3qyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyo OCA], [https://pdbe.org/3qyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qyo RCSB], [https://www.ebi.ac.uk/pdbsum/3qyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.	+	[https://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Signal transduction, regulatory processes and pharmaceutical responses are highly dependent upon ligand residence times. Gaining insight into how physical factors influence residence times (1/k(off)) should enhance our ability to manipulate biological interactions. We report experiments that yield structural insight into k(off) involving a series of eight 2,4-diaminopyrimidine inhibitors of dihydrofolate reductase whose binding affinities vary by six orders of magnitude. NMR relaxation-dispersion experiments revealed a common set of residues near the binding site that undergo a concerted millisecond-timescale switching event to a previously unidentified conformation. The rate of switching from ground to excited conformations correlates exponentially with the binding affinity K(i) and k(off), suggesting that protein dynamics serves as a mechanical initiator of ligand dissociation within this series and potentially for other macromolecule-ligand systems. Although the forward rate of conformational exchange, k(conf,forward), is faster than k(off), the use of the ligand series allowed for connections to be drawn between kinetic events on different timescales.	+
-		+
-	Evidence for dynamics in proteins as a mechanism for ligand dissociation.,Carroll MJ, Mauldin RV, Gromova AV, Singleton SF, Collins EJ, Lee AL Nat Chem Biol. 2012 Jan 15;8(3):246-52. doi: 10.1038/nchembio.769. PMID:22246400<ref>PMID:22246400</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3qyo" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Dihydrofolate reductase 3D structures\|Dihydrofolate reductase 3D structures]]		*[[Dihydrofolate reductase 3D structures\|Dihydrofolate reductase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Dihydrofolate reductase]]~~	+	[[Category: Escherichia coli K-12]]
-	[[Category: Escherichia coli k-12]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carroll~~, M J~~]]	+	[[Category: Carroll MJ]]
-	[[Category: Collins~~, E J~~]]	+	[[Category: Collins EJ]]
-	[[Category: Gromova~~, A V~~]]	+	[[Category: Gromova AV]]
-	[[Category: Lee~~, A L~~]]	+	[[Category: Lee AL]]
-	[[Category: Mauldin~~, R V~~]]	+	[[Category: Mauldin RV]]
-	[[Category: Singleton~~, S F]]~~	+	[[Category: Singleton SF]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Reductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 05:41, 15 June 2022

OCA — Wed, 15 Jun 2022 05:41:39 GMT

←Older revision		Revision as of 05:41, 15 June 2022
Line 1:		Line 1:

	==Sensitivity of receptor internal motions to ligand binding affinity and kinetic off-rate==		==Sensitivity of receptor internal motions to ligand binding affinity and kinetic off-rate==
-	<StructureSection load='3qyo' size='340' side='right' caption='[[3qyo]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='3qyo' size='340' side='right'caption='[[3qyo]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qyo]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QYO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qyo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QYO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=Q24:QUINAZOLINE-2,4-DIAMINE'>Q24</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=Q24:QUINAZOLINE-2,4-DIAMINE'>Q24</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qyl\|3qyl]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3qyl\|3qyl]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </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=3qyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyo OCA], [~~http~~://pdbe.org/3qyo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qyo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qyo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyo 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=3qyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyo OCA], [https://pdbe.org/3qyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qyo RCSB], [https://www.ebi.ac.uk/pdbsum/3qyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.	+	[[https://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]	+	*[[Dihydrofolate reductase 3D structures\|Dihydrofolate reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 29:
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
		+	[[Category: Large Structures]]
	[[Category: Carroll, M J]]		[[Category: Carroll, M J]]
	[[Category: Collins, E J]]		[[Category: Collins, E J]]

OCA at 10:20, 13 February 2019

OCA — Wed, 13 Feb 2019 10:20:07 GMT

←Older revision		Revision as of 10:20, 13 February 2019
Line 3:		Line 3:
	<StructureSection load='3qyo' size='340' side='right' caption='[[3qyo]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='3qyo' size='340' side='right' caption='[[3qyo]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qyo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QYO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qyo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QYO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=Q24:QUINAZOLINE-2,4-DIAMINE'>Q24</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=Q24:QUINAZOLINE-2,4-DIAMINE'>Q24</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qyl\|3qyl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qyl\|3qyl]]</td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli k-12]]
	[[Category: Carroll, M J]]		[[Category: Carroll, M J]]
	[[Category: Collins, E J]]		[[Category: Collins, E J]]

OCA at 00:17, 5 August 2016

OCA — Fri, 05 Aug 2016 00:17:29 GMT

←Older revision		Revision as of 00:17, 5 August 2016
Line 1:		Line 1:
		+
	==Sensitivity of receptor internal motions to ligand binding affinity and kinetic off-rate==		==Sensitivity of receptor internal motions to ligand binding affinity and kinetic off-rate==
	<StructureSection load='3qyo' size='340' side='right' caption='[[3qyo]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='3qyo' size='340' side='right' caption='[[3qyo]], [[Resolution\|resolution]] 2.09Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qyl\|3qyl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qyl\|3qyl]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </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=3qyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qyo RCSB], [http://www.ebi.ac.uk/pdbsum/3qyo PDBsum]</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=3qyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyo OCA], [http://pdbe.org/3qyo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qyo RCSB], [http://www.ebi.ac.uk/pdbsum/3qyo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3qyo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 21:06, 24 December 2014

OCA — Wed, 24 Dec 2014 21:06:11 GMT

←Older revision		Revision as of 21:06, 24 December 2014
Line 2:		Line 2:
	<StructureSection load='3qyo' size='340' side='right' caption='[[3qyo]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='3qyo' size='340' side='right' caption='[[3qyo]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qyo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QYO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qyo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QYO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=Q24:QUINAZOLINE-2,4-DIAMINE'>Q24</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=Q24:QUINAZOLINE-2,4-DIAMINE'>Q24</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qyl\|3qyl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qyl\|3qyl]]</td></tr>
Line 8:		Line 8:
	<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=3qyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qyo RCSB], [http://www.ebi.ac.uk/pdbsum/3qyo PDBsum]</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=3qyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qyo RCSB], [http://www.ebi.ac.uk/pdbsum/3qyo PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
-	[[Category: ~~Escherichia coli k-12~~]]	+	[[Category: Ecoli]]
	[[Category: Carroll, M J]]		[[Category: Carroll, M J]]
	[[Category: Collins, E J]]		[[Category: Collins, E J]]

OCA at 07:29, 12 November 2014

OCA — Wed, 12 Nov 2014 07:29:03 GMT

←Older revision		Revision as of 07:29, 12 November 2014
Line 25:		Line 25:
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
-	[[Category: Carroll, M J.]]	+	[[Category: Carroll, M J]]
-	[[Category: Collins, E J.]]	+	[[Category: Collins, E J]]
-	[[Category: Gromova, A V.]]	+	[[Category: Gromova, A V]]
-	[[Category: Lee, A L.]]	+	[[Category: Lee, A L]]
-	[[Category: Mauldin, R V.]]	+	[[Category: Mauldin, R V]]
-	[[Category: Singleton, S F.]]	+	[[Category: Singleton, S F]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Reductase]]		[[Category: Reductase]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]

OCA at 14:18, 3 November 2014

OCA — Mon, 03 Nov 2014 14:18:35 GMT

←Older revision		Revision as of 14:18, 3 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3qyo.~~png~~\|~~left~~\|~~200px~~]]	+	==Sensitivity of receptor internal motions to ligand binding affinity and kinetic off-rate==
		+	<StructureSection load='3qyo' size='340' side='right' caption='[[3qyo]], [[Resolution\|resolution]] 2.09Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3qyo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QYO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=Q24:QUINAZOLINE-2,4-DIAMINE'>Q24</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qyl\|3qyl]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </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=3qyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qyo RCSB], [http://www.ebi.ac.uk/pdbsum/3qyo PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Signal transduction, regulatory processes and pharmaceutical responses are highly dependent upon ligand residence times. Gaining insight into how physical factors influence residence times (1/k(off)) should enhance our ability to manipulate biological interactions. We report experiments that yield structural insight into k(off) involving a series of eight 2,4-diaminopyrimidine inhibitors of dihydrofolate reductase whose binding affinities vary by six orders of magnitude. NMR relaxation-dispersion experiments revealed a common set of residues near the binding site that undergo a concerted millisecond-timescale switching event to a previously unidentified conformation. The rate of switching from ground to excited conformations correlates exponentially with the binding affinity K(i) and k(off), suggesting that protein dynamics serves as a mechanical initiator of ligand dissociation within this series and potentially for other macromolecule-ligand systems. Although the forward rate of conformational exchange, k(conf,forward), is faster than k(off), the use of the ligand series allowed for connections to be drawn between kinetic events on different timescales.

-	~~{{STRUCTURE_3qyo\| PDB=3qyo \| SCENE= }}~~	+	Evidence for dynamics in proteins as a mechanism for ligand dissociation.,Carroll MJ, Mauldin RV, Gromova AV, Singleton SF, Collins EJ, Lee AL Nat Chem Biol. 2012 Jan 15;8(3):246-52. doi: 10.1038/nchembio.769. PMID:22246400<ref>PMID:22246400</ref>

-	~~===Sensitivity~~ of ~~receptor internal motions to ligand binding affinity and kinetic off-rate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22246400}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3qyo]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA].~~	+

	==See Also==		==See Also==
	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]		*[[Dihydrofolate reductase\|Dihydrofolate reductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:022246400<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
Line 25:		Line 33:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Reductase]]		[[Category: Reductase]]
-	[[Category: ~~Rossman~~ fold]]	+	[[Category: Rossmann fold]]

OCA at 09:08, 20 October 2012

OCA — Sat, 20 Oct 2012 09:08:02 GMT

←Older revision		Revision as of 09:08, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3qyo]] is a 1 chain structure ~~of [[Dihydrofolate reductase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA].	+	[[3qyo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA].

	==See Also==		==See Also==

OCA at 21:51, 25 July 2012

OCA — Wed, 25 Jul 2012 21:51:11 GMT

←Older revision		Revision as of 21:51, 25 July 2012
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	[[Image:3qyo.png\|left\|200px]]		[[Image:3qyo.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_3qyo\| PDB=3qyo \| SCENE= }}		{{STRUCTURE_3qyo\| PDB=3qyo \| SCENE= }}

	===Sensitivity of receptor internal motions to ligand binding affinity and kinetic off-rate===		===Sensitivity of receptor internal motions to ligand binding affinity and kinetic off-rate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22246400}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_22246400}}		{{ABSTRACT_PUBMED_22246400}}

	==About this Structure==		==About this Structure==
-	[[3qyo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA].	+	[[3qyo]] is a 1 chain structure of [[Dihydrofolate reductase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA].
		+
		+	==See Also==
		+	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]

	==Reference==		==Reference==

OCA at 08:08, 25 April 2012

OCA — Wed, 25 Apr 2012 08:08:42 GMT

←Older revision		Revision as of 08:08, 25 April 2012
Line 1:		Line 1:
-	[[Image:3qyo.~~jpg~~\|left\|200px]]	+	[[Image:3qyo.png\|left\|200px]]

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	===Sensitivity of receptor internal motions to ligand binding affinity and kinetic off-rate===		===Sensitivity of receptor internal motions to ligand binding affinity and kinetic off-rate===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22246400}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22246400 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22246400}}

	==About this Structure==		==About this Structure==
	[[3qyo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA].		[[3qyo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYO OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022246400</ref><references group="xtra"/>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]