6kcm - Revision history

OCA at 10:30, 22 November 2023

OCA — Wed, 22 Nov 2023 10:30:16 GMT

←Older revision		Revision as of 10:30, 22 November 2023
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	<StructureSection load='6kcm' size='340' side='right'caption='[[6kcm]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6kcm' size='340' side='right'caption='[[6kcm]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kcm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Plafa Plafa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KCM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KCM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kcm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KCM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KCM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PE0:PTERINE'>PE0</scene>, <scene name='pdbligand=PHB:P-HYDROXYBENZOIC+ACID'>PHB</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]] 2.3Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPPK-DHPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5833 PLAFA])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PE0:PTERINE'>PE0</scene>, <scene name='pdbligand=PHB:P-HYDROXYBENZOIC+ACID'>PHB</scene></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=6kcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kcm OCA], [~~http~~://pdbe.org/6kcm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kcm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kcm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kcm 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=6kcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kcm OCA], [https://pdbe.org/6kcm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kcm RCSB], [https://www.ebi.ac.uk/pdbsum/6kcm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kcm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q25704_PLAFA Q25704_PLAFA]
	<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 6kcm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6kcm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dihydropteroate synthase 3D structures\|Dihydropteroate synthase 3D structures]]
		+	*[[HPPK 3D structures\|HPPK 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Plafa~~]]	+	[[Category: Plasmodium falciparum]]
-	[[Category: Chitnumsub, P]]	+	[[Category: Chitnumsub P]]
-	[[Category: Jaruwat, A]]	+	[[Category: Jaruwat A]]
-	[[Category: Yuthavong, Y]]	+	[[Category: Yuthavong Y]]
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Tim barrel]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:29, 19 August 2020

OCA — Wed, 19 Aug 2020 06:29:43 GMT

←Older revision		Revision as of 06:29, 19 August 2020
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	<StructureSection load='6kcm' size='340' side='right'caption='[[6kcm]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6kcm' size='340' side='right'caption='[[6kcm]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kcm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KCM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KCM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kcm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Plafa Plafa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KCM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KCM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PE0:PTERINE'>PE0</scene>, <scene name='pdbligand=PHB:P-HYDROXYBENZOIC+ACID'>PHB</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PE0:PTERINE'>PE0</scene>, <scene name='pdbligand=PHB:P-HYDROXYBENZOIC+ACID'>PHB</scene></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=6kcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kcm OCA], [http://pdbe.org/6kcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kcm RCSB], [http://www.ebi.ac.uk/pdbsum/6kcm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kcm ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPPK-DHPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5833 PLAFA])</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=6kcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kcm OCA], [http://pdbe.org/6kcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kcm RCSB], [http://www.ebi.ac.uk/pdbsum/6kcm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kcm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Plafa]]
	[[Category: Chitnumsub, P]]		[[Category: Chitnumsub, P]]
	[[Category: Jaruwat, A]]		[[Category: Jaruwat, A]]

OCA at 04:11, 13 February 2020

OCA — Thu, 13 Feb 2020 04:11:41 GMT

←Older revision		Revision as of 04:11, 13 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kcm is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Plasmodium falciparum HPPK-DHPS S436F/A437G/A613S with pterin and p-hydrobenzoate==
		+	<StructureSection load='6kcm' size='340' side='right'caption='[[6kcm]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6kcm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KCM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KCM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PE0:PTERINE'>PE0</scene>, <scene name='pdbligand=PHB:P-HYDROXYBENZOIC+ACID'>PHB</scene></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=6kcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kcm OCA], [http://pdbe.org/6kcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kcm RCSB], [http://www.ebi.ac.uk/pdbsum/6kcm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kcm ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The clinical efficacy of sulfa drugs as antimalarials has declined owing to the evolution of resistance in Plasmodium falciparum (Pf) malaria parasites. In order to understand the basis of this resistance and to design more effective antimalarials, we have solved 13 structures of the bifunctional enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK)-dihydropteroate synthase (DHPS) from wild-type (WT) P. falciparum and sulfa-resistant mutants, both as apoenzyme and as complexes with pteroate (PTA) and sulfa derivatives. The structures of these complexes show that PTA, which effectively inhibits both the WT and mutants, stays in active sites without steric constraint. In contrast, parts of the sulfa compounds situated outside of the substrate envelope are in the vicinity of the resistance mutations. Steric conflict between compound and mutant residue along with increased flexibility of loop D2 in the mutants can account for the reduced compound binding affinity to the mutants. Kinetic data show that the mutants have enhanced enzyme activity compared with the WT. These PfDHPS structural insights are critical for the design of novel, substrate envelope-compliant DHPS inhibitors that are less vulnerable to resistance mutations. DATABASES: The data reported in this paper have been deposited in the Protein Data Bank, www.wwpdb.org. PDB ID codes: 6JWQ for apoWT; 6JWR, 6JWS, and 6JWT for PTA complexes of WT, A437G (3D7), and V1/S; 6JWU, 6JWV, and 6JWW for STZ-DHP complexes of WT, 3D7, and V1/S; 6JWX, 6JWY, and 6JWZ for SDX-DHP complexes of WT, 3D7, and W2; 6KCK, 6KCL, and 6KCM for Pterin/pHBA complexes of WT, TN1, and W2.

-	~~Authors: Chitnumsub~~, P., Jaruwat, A., ~~Yuthavong~~, Y.	+	The structure of Plasmodium falciparum hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase reveals the basis of sulfa resistance.,Chitnumsub P, Jaruwat A, Talawanich Y, Noytanom K, Liwnaree B, Poen S, Yuthavong Y FEBS J. 2019 Dec 28. doi: 10.1111/febs.15196. PMID:31883412<ref>PMID:31883412</ref>

-	~~Description: Crystal structure~~ of ~~Plasmodium falciparum HPPK~~-~~DHPS S436F~~/~~A437G~~/~~A613S with pterin and p-hydrobenzoate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Yuthavong, Y]]~~	+	<div class="pdbe-citations 6kcm" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Jaruwat, A~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Chitnumsub, P]]		[[Category: Chitnumsub, P]]
		+	[[Category: Jaruwat, A]]
		+	[[Category: Yuthavong, Y]]
		+	[[Category: Kinase]]
		+	[[Category: Tim barrel]]
		+	[[Category: Transferase]]

OCA at 08:41, 17 July 2019

OCA — Wed, 17 Jul 2019 08:41:08 GMT

←Older revision		Revision as of 08:41, 17 July 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Chitnumsub, P., Jaruwat, A., Yuthavong, Y.		Authors: Chitnumsub, P., Jaruwat, A., Yuthavong, Y.

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

OCA — Wed, 03 Jul 2019 04:09:38 GMT

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

←Older revision

Revision as of 04:09, 3 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kcm is ON HOLD Authors: Chitnumsub, P., Jaruwat, A., Yuthavong, Y. Description: Crystal structure of Plasmodium falciparum HPPK-DHPS S436F/A437G/A...

OCA — Wed, 03 Jul 2019 04:09:37 GMT

New page: '''Unreleased structure''' The entry 6kcm is ON HOLD Authors: Chitnumsub, P., Jaruwat, A., Yuthavong, Y. Description: Crystal structure of Plasmodium falciparum HPPK-DHPS S436F/A437G/A...

New page

'''Unreleased structure'''

The entry 6kcm is ON HOLD

Authors: Chitnumsub, P., Jaruwat, A., Yuthavong, Y.

Description: Crystal structure of Plasmodium falciparum HPPK-DHPS S436F/A437G/A613S with pterin and p-hydrobenzoate
[[Category: Unreleased Structures]]
[[Category: Yuthavong, Y]]
[[Category: Jaruwat, A]]
[[Category: Chitnumsub, P]]