3fyv - Revision history

OCA at 08:25, 20 March 2024

OCA — Wed, 20 Mar 2024 08:25:49 GMT

←Older revision		Revision as of 08:25, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3fyv' size='340' side='right'caption='[[3fyv]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3fyv' size='340' side='right'caption='[[3fyv]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fyv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fyv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FYV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=XCF:5-[[(2R)-2-CYCLOPROPYL-7,8-DIMETHOXY-2H-CHROMEN-5-YL]METHYL]PYRIMIDINE-2,4-DIAMINE'>XCF</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]] 2.2Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fy8\|3fy8]], [[3fy9\|3fy9]], [[3fyw\|3fyw]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=XCF:5-[[(2R)-2-CYCLOPROPYL-7,8-DIMETHOXY-2H-CHROMEN-5-YL]METHYL]PYRIMIDINE-2,4-DIAMINE'>XCF</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=3fyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyv OCA], [https://pdbe.org/3fyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fyv RCSB], [https://www.ebi.ac.uk/pdbsum/3fyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyv 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=3fyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyv OCA], [https://pdbe.org/3fyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fyv RCSB], [https://www.ebi.ac.uk/pdbsum/3fyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DYR_STAAU DYR_STAAU]] 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_STAAU DYR_STAAU] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3fyv ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3fyv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Iclaprim is a novel dihydrofolate reductase (DHFR) inhibitor belonging to the 2,4-diaminopyrimidine class of antibiotics, of which trimethoprim (TMP) is the most well known representative. Iclaprim exhibits potent bactericidal activity against major Gram-positive pathogens, notably methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) phenotypes, including TMP-resistant strains. The inhibition properties of racemic iclaprim and of the two enantiomers, termed AR-101 and AR-102, towards S. aureus wild-type DHFR and TMP-resistant F98Y mutant DHFR were determined and compared. Similar to TMP, AR-101, AR-102 and iclaprim are all competitive inhibitors with respect to the substrate dihydrofolate. Iclaprim, AR-101 and AR-102 demonstrated little or no difference in activity towards these enzymes and were significantly more potent than TMP. The crystal structures of S. aureus DHFR and F98Y mutant DHFR were determined as ternary complexes with NADPH and either AR-101, AR-102 or iclaprim. The binding modes of the inhibitors were analysed and compared. The X-ray crystallographic data explain the binding modes of all molecules well and can be used to rationalize the equipotent affinity of AR-101, AR-102 and iclaprim, which is also reflected in their antibacterial properties.
-
-	Inhibitory properties and X-ray crystallographic study of the binding of AR-101, AR-102 and iclaprim in ternary complexes with NADPH and dihydrofolate reductase from Staphylococcus aureus.,Oefner C, Parisi S, Schulz H, Lociuro S, Dale GE Acta Crystallogr D Biol Crystallogr. 2009 Aug;65(Pt 8):751-7. Epub 2009, Jul 10. PMID:19622858<ref>PMID:19622858</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3fyv" 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: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Oefner, C~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: ~~Ar-102]]~~	+	[[Category: Oefner C]]
-	~~[[Category: Dhfr]]~~	+
-	~~[[Category: Nadp]]~~	+
-	~~[[Category: One-carbon metabolism]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Staph aureus~~]]	+

OCA at 07:51, 9 March 2022

OCA — Wed, 09 Mar 2022 07:51:30 GMT

←Older revision		Revision as of 07:51, 9 March 2022
Line 1:		Line 1:

	==Staph. aureus DHFR complexed with NADPH and AR-102==		==Staph. aureus DHFR complexed with NADPH and AR-102==
-	<StructureSection load='3fyv' size='340' side='right' caption='[[3fyv]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='3fyv' size='340' side='right'caption='[[3fyv]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fyv]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3FYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fyv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FYV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=XCF:5-[[(2R)-2-CYCLOPROPYL-7,8-DIMETHOXY-2H-CHROMEN-5-YL]METHYL]PYRIMIDINE-2,4-DIAMINE'>XCF</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=XCF:5-[[(2R)-2-CYCLOPROPYL-7,8-DIMETHOXY-2H-CHROMEN-5-YL]METHYL]PYRIMIDINE-2,4-DIAMINE'>XCF</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fy8\|3fy8]], [[3fy9\|3fy9]], [[3fyw\|3fyw]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fy8\|3fy8]], [[3fy9\|3fy9]], [[3fyw\|3fyw]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=3fyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyv OCA], [~~http~~://pdbe.org/3fyv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3fyv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3fyv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyv 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=3fyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyv OCA], [https://pdbe.org/3fyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fyv RCSB], [https://www.ebi.ac.uk/pdbsum/3fyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DYR_STAAU DYR_STAAU]] 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_STAAU DYR_STAAU]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]	+	*[[Dihydrofolate reductase 3D structures\|Dihydrofolate reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
		+	[[Category: Large Structures]]
	[[Category: Oefner, C]]		[[Category: Oefner, C]]
	[[Category: Ar-102]]		[[Category: Ar-102]]

OCA at 07:19, 5 December 2018

OCA — Wed, 05 Dec 2018 07:19:49 GMT

←Older revision		Revision as of 07:19, 5 December 2018
Line 1:		Line 1:
		+
	==Staph. aureus DHFR complexed with NADPH and AR-102==		==Staph. aureus DHFR complexed with NADPH and AR-102==
	<StructureSection load='3fyv' size='340' side='right' caption='[[3fyv]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3fyv' size='340' side='right' caption='[[3fyv]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=3fyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyv OCA], [http://pdbe.org/3fyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fyv RCSB], [http://www.ebi.ac.uk/pdbsum/3fyv 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=3fyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyv OCA], [http://pdbe.org/3fyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fyv RCSB], [http://www.ebi.ac.uk/pdbsum/3fyv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fy/3fyv_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fy/3fyv_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 19:30, 8 February 2016

OCA — Mon, 08 Feb 2016 19:30:26 GMT

←Older revision		Revision as of 19:30, 8 February 2016
Line 7:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=3fyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fyv RCSB], [http://www.ebi.ac.uk/pdbsum/3fyv 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=3fyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyv OCA], [http://pdbe.org/3fyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fyv RCSB], [http://www.ebi.ac.uk/pdbsum/3fyv PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3fyv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3fyv" style="background-color:#fffaf0;"></div>

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

OCA at 01:39, 25 December 2014

OCA — Thu, 25 Dec 2014 01:39:19 GMT

←Older revision		Revision as of 01:39, 25 December 2014
Line 9:		Line 9:
	<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=3fyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fyv RCSB], [http://www.ebi.ac.uk/pdbsum/3fyv 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=3fyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fyv RCSB], [http://www.ebi.ac.uk/pdbsum/3fyv PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DYR_STAAU DYR_STAAU]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:36, 21 December 2014

OCA — Sun, 21 Dec 2014 06:36:43 GMT

←Older revision		Revision as of 06:36, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3fyv~~\| ~~PDB~~=3fyv \| ~~SCENE~~= }}	+	==Staph. aureus DHFR complexed with NADPH and AR-102==
-	===~~Staph~~. aureus ~~DHFR complexed~~ with ~~NADPH~~ and AR-~~102~~===	+	<StructureSection load='3fyv' size='340' side='right' caption='[[3fyv]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19622858}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3fyv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FYV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=XCF:5-[[(2R)-2-CYCLOPROPYL-7,8-DIMETHOXY-2H-CHROMEN-5-YL]METHYL]PYRIMIDINE-2,4-DIAMINE'>XCF</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fy8\|3fy8]], [[3fy9\|3fy9]], [[3fyw\|3fyw]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=3fyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fyv RCSB], [http://www.ebi.ac.uk/pdbsum/3fyv PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fy/3fyv_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Iclaprim is a novel dihydrofolate reductase (DHFR) inhibitor belonging to the 2,4-diaminopyrimidine class of antibiotics, of which trimethoprim (TMP) is the most well known representative. Iclaprim exhibits potent bactericidal activity against major Gram-positive pathogens, notably methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) phenotypes, including TMP-resistant strains. The inhibition properties of racemic iclaprim and of the two enantiomers, termed AR-101 and AR-102, towards S. aureus wild-type DHFR and TMP-resistant F98Y mutant DHFR were determined and compared. Similar to TMP, AR-101, AR-102 and iclaprim are all competitive inhibitors with respect to the substrate dihydrofolate. Iclaprim, AR-101 and AR-102 demonstrated little or no difference in activity towards these enzymes and were significantly more potent than TMP. The crystal structures of S. aureus DHFR and F98Y mutant DHFR were determined as ternary complexes with NADPH and either AR-101, AR-102 or iclaprim. The binding modes of the inhibitors were analysed and compared. The X-ray crystallographic data explain the binding modes of all molecules well and can be used to rationalize the equipotent affinity of AR-101, AR-102 and iclaprim, which is also reflected in their antibacterial properties.

-	~~==Function==~~	+	Inhibitory properties and X-ray crystallographic study of the binding of AR-101, AR-102 and iclaprim in ternary complexes with NADPH and dihydrofolate reductase from Staphylococcus aureus.,Oefner C, Parisi S, Schulz H, Lociuro S, Dale GE Acta Crystallogr D Biol Crystallogr. 2009 Aug;65(Pt 8):751-7. Epub 2009, Jul 10. PMID:19622858<ref>PMID:19622858</ref>
-	~~[[http://www~~.~~uniprot~~.~~org/uniprot/DYR_STAAU DYR_STAAU]] Key enzyme in folate metabolism~~. ~~Catalyzes an essential reaction for de novo glycine and purine synthesis~~, ~~and for DNA precursor synthesis~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3fyv]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3FYV OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]		*[[Dihydrofolate reductase\|Dihydrofolate reductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:019622858</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
-	[[Category: Oefner, C.]]	+	[[Category: Oefner, C]]
	[[Category: Ar-102]]		[[Category: Ar-102]]
	[[Category: Dhfr]]		[[Category: Dhfr]]

OCA at 11:42, 20 November 2013

OCA — Wed, 20 Nov 2013 11:42:38 GMT

←Older revision		Revision as of 11:42, 20 November 2013
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-	[[Image:3fyv.png\|left\|200px]]
-
	{{STRUCTURE_3fyv\| PDB=3fyv \| SCENE= }}		{{STRUCTURE_3fyv\| PDB=3fyv \| SCENE= }}
-
	===Staph. aureus DHFR complexed with NADPH and AR-102===		===Staph. aureus DHFR complexed with NADPH and AR-102===
		+	{{ABSTRACT_PUBMED_19622858}}

-	~~{{ABSTRACT_PUBMED_19622858}}~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/DYR_STAAU DYR_STAAU]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.

	==About this Structure==		==About this Structure==
-	[[3fyv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_aureus Staphylococcus~~ aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYV OCA].	+	[[3fyv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYV OCA].

	==See Also==		==See Also==
Line 14:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:019622858</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019622858</ref><references group="xtra"/><references/>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
-	[[Category: Staphylococcus aureus]]
	[[Category: Oefner, C.]]		[[Category: Oefner, C.]]
	[[Category: Ar-102]]		[[Category: Ar-102]]

OCA at 11:14, 20 October 2012

OCA — Sat, 20 Oct 2012 11:14:06 GMT

←Older revision		Revision as of 11:14, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3fyv]] is a 1 chain structure ~~of [[Dihydrofolate reductase]]~~ with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYV OCA].	+	[[3fyv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYV OCA].

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

OCA at 04:40, 26 July 2012

OCA — Thu, 26 Jul 2012 04:40:28 GMT

←Older revision		Revision as of 04:40, 26 July 2012
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	[[Image:3fyv.png\|left\|200px]]		[[Image:3fyv.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3fyv", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3fyv\| PDB=3fyv \| SCENE= }}		{{STRUCTURE_3fyv\| PDB=3fyv \| SCENE= }}

	===Staph. aureus DHFR complexed with NADPH and AR-102===		===Staph. aureus DHFR complexed with NADPH and AR-102===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19622858}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19622858 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19622858}}		{{ABSTRACT_PUBMED_19622858}}

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	==See Also==		==See Also==
-	*[[Dihydrofolate reductase]]	+	*[[Dihydrofolate reductase\|Dihydrofolate reductase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19622858~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019622858</ref><references group="xtra"/>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]

OCA: Protected "3fyv" [edit=sysop:move=sysop]

OCA — Mon, 27 Dec 2010 02:14:06 GMT

Protected "3fyv" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:14, 27 December 2010