1q1y - Revision history

OCA at 06:00, 17 April 2024

OCA — Wed, 17 Apr 2024 06:00:41 GMT

←Older revision		Revision as of 06:00, 17 April 2024
Line 3:		Line 3:
	<StructureSection load='1q1y' size='340' side='right'caption='[[1q1y]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1q1y' size='340' side='right'caption='[[1q1y]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q1y]] 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=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q1y]] 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=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BB2:ACTINONIN'>BB2</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]] 1.9Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~CSD~~:~~3-SULFINOALANINE~~'>~~CSD~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</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">SA1100 ([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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [https://pdbe.org/1q1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [https://www.ebi.ac.uk/pdbsum/1q1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1y ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88]~~ </~~span~~></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=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [~~http~~://pdbe.org/1q1y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1q1y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1y ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DEF_STAAU DEF_STAAU]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).[HAMAP-Rule:MF_00163]	+	[https://www.uniprot.org/uniprot/DEF_STAAU DEF_STAAU] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).[HAMAP-Rule:MF_00163]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 25:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Peptide deformylase]]
-	[[Category: Kim, H L]]
-	[[Category: Kim, H W]]
-	[[Category: Lee, J Y]]
-	[[Category: Lee, S K]]
-	[[Category: Mikami, B]]
-	[[Category: Suh, S W]]
-	[[Category: Yoon, H J]]
-	[[Category: Actinonin]]
-	[[Category: Hydrolase]]
-	[[Category: Metallo-enzyme]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
		+	[[Category: Kim HL]]
		+	[[Category: Kim HW]]
		+	[[Category: Lee JY]]
		+	[[Category: Lee SK]]
		+	[[Category: Mikami B]]
		+	[[Category: Suh SW]]
		+	[[Category: Yoon HJ]]

OCA at 07:41, 9 December 2020

OCA — Wed, 09 Dec 2020 07:41:28 GMT

←Older revision		Revision as of 07:41, 9 December 2020
Line 1:		Line 1:

	==Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin==		==Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin==
-	<StructureSection load='1q1y' size='340' side='right' caption='[[1q1y]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1q1y' size='340' side='right'caption='[[1q1y]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q1y]] 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=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q1y]] 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=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</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=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1100 ([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">SA1100 ([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/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [http://pdbe.org/1q1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [http://www.ebi.ac.uk/pdbsum/1q1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1y ProSAT]</span></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=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [http://pdbe.org/1q1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [http://www.ebi.ac.uk/pdbsum/1q1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Kim, H L]]		[[Category: Kim, H L]]

OCA at 08:06, 12 December 2018

OCA — Wed, 12 Dec 2018 08:06:46 GMT

←Older revision		Revision as of 08:06, 12 December 2018
Line 3:		Line 3:
	<StructureSection load='1q1y' size='340' side='right' caption='[[1q1y]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1q1y' size='340' side='right' caption='[[1q1y]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q1y]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q1y]] 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=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</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=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1100 ([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/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [http://pdbe.org/1q1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [http://www.ebi.ac.uk/pdbsum/1q1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1y ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [http://pdbe.org/1q1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [http://www.ebi.ac.uk/pdbsum/1q1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1y ProSAT]</span></td></tr>
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/q1/1q1y_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/1q1y_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 07:48, 9 March 2017

OCA — Thu, 09 Mar 2017 07:48:31 GMT

←Older revision		Revision as of 07:48, 9 March 2017
Line 1:		Line 1:
		+
	==Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin==		==Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin==
	<StructureSection load='1q1y' size='340' side='right' caption='[[1q1y]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1q1y' size='340' side='right' caption='[[1q1y]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q1y]] 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=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q1y]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</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=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1100 ([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/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [http://pdbe.org/1q1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [http://www.ebi.ac.uk/pdbsum/1q1y 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=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [http://pdbe.org/1q1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [http://www.ebi.ac.uk/pdbsum/1q1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1y ProSAT]</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=1q1y ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	__TOC__		__TOC__

OCA at 13:55, 11 September 2015

OCA — Fri, 11 Sep 2015 13:55:54 GMT

←Older revision		Revision as of 13:55, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1q1y' size='340' side='right' caption='[[1q1y]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1q1y' size='340' side='right' caption='[[1q1y]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q1y]] 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=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q1y]] 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=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</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=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1100 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 ~~Staphylococcus~~ aureus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1100 ([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/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [http://www.ebi.ac.uk/pdbsum/1q1y 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=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [http://pdbe.org/1q1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [http://www.ebi.ac.uk/pdbsum/1q1y PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
-	[[Category: Staphylococcus aureus]]
	[[Category: Kim, H L]]		[[Category: Kim, H L]]
	[[Category: Kim, H W]]		[[Category: Kim, H W]]
Line 35:		Line 34:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Metallo-enzyme]]		[[Category: Metallo-enzyme]]
		+	[[Category: Staphylococcus aureus]]

OCA at 17:22, 25 December 2014

OCA — Thu, 25 Dec 2014 17:22:51 GMT

←Older revision		Revision as of 17:22, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1q1y]] 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=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[1q1y]] 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=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1100 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1100 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [http://www.ebi.ac.uk/pdbsum/1q1y 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=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [http://www.ebi.ac.uk/pdbsum/1q1y PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DEF_STAAU DEF_STAAU]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).[HAMAP-Rule:MF_00163]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 23:		Line 25:
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
-	[[Category: Kim, H L.]]	+	[[Category: Kim, H L]]
-	[[Category: Kim, H W.]]	+	[[Category: Kim, H W]]
-	[[Category: Lee, J Y.]]	+	[[Category: Lee, J Y]]
-	[[Category: Lee, S K.]]	+	[[Category: Lee, S K]]
-	[[Category: Mikami, B.]]	+	[[Category: Mikami, B]]
-	[[Category: Suh, S W.]]	+	[[Category: Suh, S W]]
-	[[Category: Yoon, H J.]]	+	[[Category: Yoon, H J]]
	[[Category: Actinonin]]		[[Category: Actinonin]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Metallo-enzyme]]		[[Category: Metallo-enzyme]]
-	[[Category: Peptide deformylase]]
-	[[Category: Staphylococcus aureus]]

OCA at 16:06, 29 September 2014

OCA — Mon, 29 Sep 2014 16:06:12 GMT

←Older revision		Revision as of 16:06, 29 September 2014
Line 1:		Line 1:
-	~~[[Image:1q1y.png\|left\|200px]]~~	+	==Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin==
-		+	<StructureSection load='1q1y' size='340' side='right' caption='[[1q1y]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{STRUCTURE_1q1y\| PDB=1q1y \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[1q1y]] 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=1Q1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1Y FirstGlance]. <br>
-	===Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin===	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
-		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
-		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1100 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>
-	==~~About this Structure~~==	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>
-	[[1q1y]] 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=1Q1Y OCA].	+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q1y RCSB], [http://www.ebi.ac.uk/pdbsum/1q1y PDBsum]</span></td></tr>
-		+	<table>
-	==~~Reference~~==	+	== Evolutionary Conservation ==
-	<~~ref group~~="~~xtra~~">~~PMID~~:~~015382235~~</~~ref~~><~~references group~~="~~xtra~~"/>	+	[[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/q1/1q1y_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>
		+	__TOC__
		+	</StructureSection>
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]

OCA: Protected "1q1y" [edit=sysop:move=sysop]

OCA — Wed, 02 Jan 2013 09:51:43 GMT

Protected "1q1y" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:51, 2 January 2013

OCA at 09:51, 2 January 2013

OCA — Wed, 02 Jan 2013 09:51:41 GMT

←Older revision		Revision as of 09:51, 2 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1q1y.png\|left\|200px]]		[[Image:1q1y.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1q1y", 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_1q1y\| PDB=1q1y \| SCENE= }}		{{STRUCTURE_1q1y\| PDB=1q1y \| SCENE= }}

Line 14:		Line 7:

	==About this Structure==		==About this Structure==
-	~~1Q1Y~~ is a 1 chain structure of 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=1Q1Y OCA].	+	[[1q1y]] 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=1Q1Y OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15382235~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015382235</ref><references group="xtra"/>
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
Line 28:		Line 21:
	[[Category: Yoon, H J.]]		[[Category: Yoon, H J.]]
	[[Category: Actinonin]]		[[Category: Actinonin]]
		+	[[Category: Hydrolase]]
	[[Category: Metallo-enzyme]]		[[Category: Metallo-enzyme]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:04:48 2009''

OCA at 22:04, 17 February 2009

OCA — Tue, 17 Feb 2009 22:04:49 GMT

←Older revision		Revision as of 22:04, 17 February 2009
Line 14:		Line 14:

	==About this Structure==		==About this Structure==
-	1Q1Y is a ~~[[Single protein]]~~ structure of 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=1Q1Y OCA].	+	1Q1Y is a 1 chain structure of 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=1Q1Y OCA].

	==Reference==		==Reference==
-	Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent., Yoon HJ, Kim HL, Lee SK, Kim HW, Kim HW, Lee JY, Mikami B, Suh SW, Proteins. 2004 Nov 15;57(3):639-42. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15382235 15382235]~~	+	<ref group="xtra">PMID:15382235</ref><references group="xtra"/>
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
-	[[Category: Single protein]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
	[[Category: Kim, H L.]]		[[Category: Kim, H L.]]
Line 33:		Line 32:
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 07~~:23:~~31 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:04:48 2009''