3ieq - Revision history

OCA at 19:21, 29 May 2024

OCA — Wed, 29 May 2024 19:21:11 GMT

←Older revision		Revision as of 19:21, 29 May 2024
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[3ieq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei Burkholderia pseudomallei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ieq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei Burkholderia pseudomallei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEQ FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.1Å</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]] 2.1Å</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=CTN:4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE'>CTN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [https://pdbe.org/3ieq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [https://www.ebi.ac.uk/pdbsum/3ieq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieq 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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [https://pdbe.org/3ieq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [https://www.ebi.ac.uk/pdbsum/3ieq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieq ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:45, 6 September 2023

OCA — Wed, 06 Sep 2023 07:45:12 GMT

←Older revision		Revision as of 07:45, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3ieq' size='340' side='right'caption='[[3ieq]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3ieq' size='340' side='right'caption='[[3ieq]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ieq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_pseudomallei"_whitmore_1913 "bacillus~~ pseudomallei~~" whitmore 1913~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ieq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei Burkholderia pseudomallei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEQ 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.1Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3f0d\|3f0d]], [[3f0e\|3f0e]], [[3f0f\|3f0f]], [[3f0g\|3f0g]], [[3iew\|3iew]]</div>~~</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ispF, mecS, BPSL2098 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~28450~~ "~~Bacillus pseudomallei~~" ~~Whitmore 1913])~~<~~/td~~></tr>	+
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </~~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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [https://pdbe.org/3ieq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [https://www.ebi.ac.uk/pdbsum/3ieq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieq 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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [https://pdbe.org/3ieq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [https://www.ebi.ac.uk/pdbsum/3ieq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~ISPF_BURPS ISPF_BURPS]~~] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107]	+	[https://www.uniprot.org/uniprot/ISPF_BURP1 ISPF_BURP1] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ pseudomallei ~~whitmore 1913]]~~	+	[[Category: Burkholderia pseudomallei]]
-	~~[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Structural genomic]]
-	[[Category: Isoprene biosynthesis]]
-	[[Category: Lyase]]
-	[[Category: Metal-binding]]
-	[[Category: Niaid]]
-	[[Category: Ssgcid]]

OCA at 03:30, 21 April 2022

OCA — Thu, 21 Apr 2022 03:30:46 GMT

←Older revision		Revision as of 03:30, 21 April 2022
Line 1:		Line 1:

	==Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine==		==Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine==
-	<StructureSection load='3ieq' size='340' side='right' caption='[[3ieq]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3ieq' size='340' side='right'caption='[[3ieq]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ieq]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_pseudomallei"_whitmore_1913 "bacillus pseudomallei" whitmore 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ieq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_pseudomallei"_whitmore_1913 "bacillus pseudomallei" whitmore 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f0d\|3f0d]], [[3f0e\|3f0e]], [[3f0f\|3f0f]], [[3f0g\|3f0g]], [[3iew\|3iew]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3f0d\|3f0d]], [[3f0e\|3f0e]], [[3f0f\|3f0f]], [[3f0g\|3f0g]], [[3iew\|3iew]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispF, mecS, BPSL2098 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28450 "Bacillus pseudomallei" Whitmore 1913])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispF, mecS, BPSL2098 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28450 "Bacillus pseudomallei" Whitmore 1913])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [~~http~~://pdbe.org/3ieq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ieq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieq 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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [https://pdbe.org/3ieq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [https://www.ebi.ac.uk/pdbsum/3ieq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ISPF_BURPS ISPF_BURPS]] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107]	+	[[https://www.uniprot.org/uniprot/ISPF_BURPS ISPF_BURPS]] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107]
	== 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==
-	*[[MECDP synthase\|MECDP synthase]]	+	*[[MECDP synthase 3D structures\|MECDP synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 40:
	[[Category: Bacillus pseudomallei whitmore 1913]]		[[Category: Bacillus pseudomallei whitmore 1913]]
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
		+	[[Category: Large Structures]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Isoprene biosynthesis]]		[[Category: Isoprene biosynthesis]]

OCA at 09:46, 19 December 2018

OCA — Wed, 19 Dec 2018 09:46:07 GMT

←Older revision		Revision as of 09:46, 19 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine==		==Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine==
	<StructureSection load='3ieq' size='340' side='right' caption='[[3ieq]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3ieq' size='340' side='right' caption='[[3ieq]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispF, mecS, BPSL2098 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28450 "Bacillus pseudomallei" Whitmore 1913])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispF, mecS, BPSL2098 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28450 "Bacillus pseudomallei" Whitmore 1913])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [http://pdbe.org/3ieq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [http://www.ebi.ac.uk/pdbsum/3ieq 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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [http://pdbe.org/3ieq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [http://www.ebi.ac.uk/pdbsum/3ieq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieq 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/ie/3ieq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ie/3ieq_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 18:55, 9 February 2016

OCA — Tue, 09 Feb 2016 18:55:17 GMT

←Older revision		Revision as of 18:55, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3ieq' size='340' side='right' caption='[[3ieq]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3ieq' size='340' side='right' caption='[[3ieq]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ieq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_pseudomallei Burkholderia~~ pseudomallei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ieq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pseudomallei"_whitmore_1913 "bacillus pseudomallei" whitmore 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f0d\|3f0d]], [[3f0e\|3f0e]], [[3f0f\|3f0f]], [[3f0g\|3f0g]], [[3iew\|3iew]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f0d\|3f0d]], [[3f0e\|3f0e]], [[3f0f\|3f0f]], [[3f0g\|3f0g]], [[3iew\|3iew]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispF, mecS, BPSL2098 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28450 ~~Burkholderia~~ pseudomallei])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispF, mecS, BPSL2098 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28450 "Bacillus pseudomallei" Whitmore 1913])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [http://www.ebi.ac.uk/pdbsum/3ieq 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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [http://pdbe.org/3ieq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [http://www.ebi.ac.uk/pdbsum/3ieq 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=3ieq 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 3ieq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus pseudomallei whitmore 1913]]
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
-	[[Category: Burkholderia pseudomallei]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Isoprene biosynthesis]]		[[Category: Isoprene biosynthesis]]

OCA at 08:51, 25 December 2014

OCA — Thu, 25 Dec 2014 08:51:00 GMT

←Older revision		Revision as of 08:51, 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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [http://www.ebi.ac.uk/pdbsum/3ieq 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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [http://www.ebi.ac.uk/pdbsum/3ieq PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ISPF_BURPS ISPF_BURPS]] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 17:42, 18 December 2014

OCA — Thu, 18 Dec 2014 17:42:40 GMT

←Older revision		Revision as of 17:42, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3ieq\| PDB=3ieq \| SCENE= }}~~	+	==Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine==
-	===Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine===	+	<StructureSection load='3ieq' size='340' side='right' caption='[[3ieq]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21359640}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ieq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei Burkholderia pseudomallei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f0d\|3f0d]], [[3f0e\|3f0e]], [[3f0f\|3f0f]], [[3f0g\|3f0g]], [[3iew\|3iew]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispF, mecS, BPSL2098 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28450 Burkholderia pseudomallei])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </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=3ieq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ieq RCSB], [http://www.ebi.ac.uk/pdbsum/3ieq 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/ie/3ieq_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 ==
		+	As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.

-	~~==Function==~~	+	Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.,Begley DW, Hartley RC, Davies DR, Edwards TE, Leonard JT, Abendroth J, Burris CA, Bhandari J, Myler PJ, Staker BL, Stewart LJ J Struct Funct Genomics. 2011 Jul;12(2):63-76. Epub 2011 Feb 26. PMID:21359640<ref>PMID:21359640</ref>
-	~~[[http~~:~~//www~~.~~uniprot.org/uniprot/ISPF_BURPS ISPF_BURPS]] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP)~~, ~~two major building blocks of isoprenoid compounds~~. ~~Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate~~ (~~CDP-ME2P) to~~ 2~~-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP~~) ~~with a corresponding release of cytidine 5~~-~~monophosphate (CMP) (By similarity)~~.~~[HAMAP-Rule~~:~~MF_00107]~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3ieq]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Burkholderia_pseudomallei Burkholderia pseudomallei]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[MECDP synthase\|MECDP synthase]]		*[[MECDP synthase\|MECDP synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:021359640</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
	[[Category: Burkholderia pseudomallei]]		[[Category: Burkholderia pseudomallei]]
-	[[Category: ~~SSGCID, Seattle~~ Structural ~~Genomics Center for Infectious Disease.~~]]	+	[[Category: Structural genomic]]
	[[Category: Isoprene biosynthesis]]		[[Category: Isoprene biosynthesis]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Niaid]]		[[Category: Niaid]]
-	[[Category: Seattle structural genomics center for infectious disease]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
-	[[Category: Structural genomic]]

OCA at 08:06, 8 May 2013

OCA — Wed, 08 May 2013 08:06:09 GMT

←Older revision		Revision as of 08:06, 8 May 2013
Line 1:		Line 1:
-	[[Image:3ieq.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ieq", 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_3ieq\| PDB=3ieq \| SCENE= }}		{{STRUCTURE_3ieq\| PDB=3ieq \| SCENE= }}
-
	===Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine===		===Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine===
		+	{{ABSTRACT_PUBMED_21359640}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/ISPF_BURPS ISPF_BURPS]] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107]
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21359640}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~), ~~where 21359640 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_21359640}}~~	+

	==About this Structure==		==About this Structure==
	[[3ieq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei Burkholderia pseudomallei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA].		[[3ieq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei Burkholderia pseudomallei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA].
		+
		+	==See Also==
		+	*[[MECDP synthase\|MECDP synthase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:021359640</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021359640</ref><references group="xtra"/><references/>
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
	[[Category: Burkholderia pseudomallei]]		[[Category: Burkholderia pseudomallei]]

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

OCA — Wed, 06 Jul 2011 17:53:25 GMT

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

←Older revision

Revision as of 17:53, 6 July 2011

OCA at 17:53, 6 July 2011

OCA — Wed, 06 Jul 2011 17:53:22 GMT

←Older revision		Revision as of 17:53, 6 July 2011
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3ieq.png\|left\|200px]]
-	[[Image:3ieq.~~jpg~~\|left\|200px]]	+

	<!--		<!--
Line 12:		Line 11:
	===Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine===		===Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21359640}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21359640 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21359640}}

	==About this Structure==		==About this Structure==
-	~~3IEQ~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei Burkholderia pseudomallei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA].	+	[[3ieq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei Burkholderia pseudomallei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEQ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021359640</ref><references group="xtra"/>
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
	[[Category: Burkholderia pseudomallei]]		[[Category: Burkholderia pseudomallei]]
Line 25:		Line 33:
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 5 11:07:44 2009''