3b3b - Revision history

OCA at 12:01, 30 August 2023

2023-08-30T12:01:20Z

←Older revision		Revision as of 12:01, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='3b3b' size='340' side='right'caption='[[3b3b]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3b3b' size='340' side='right'caption='[[3b3b]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b3b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B3B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b3b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B3B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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]] 1.85Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3b2p\|3b2p]], [[2hpo\|2hpo]], [[2hpt\|2hpt]], [[3b2x\|3b2x]], [[3b34\|3b34]], [[3b37\|3b37]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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">Aminopeptidase N ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </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=3b3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3b OCA], [https://pdbe.org/3b3b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b3b RCSB], [https://www.ebi.ac.uk/pdbsum/3b3b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b3b 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=3b3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3b OCA], [https://pdbe.org/3b3b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b3b RCSB], [https://www.ebi.ac.uk/pdbsum/3b3b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b3b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AMPN_ECOLI AMPN_ECOLI]] Aminopeptidase N is involved in the degradation of intracellular peptides generated by protein breakdown during normal growth as well as in response to nutrient starvation.	+	[https://www.uniprot.org/uniprot/AMPN_ECOLI AMPN_ECOLI] Aminopeptidase N is involved in the degradation of intracellular peptides generated by protein breakdown during normal growth as well as in response to nutrient starvation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Membrane alanyl aminopeptidase]]~~	+	[[Category: Addlagatta A]]
-	[[Category: Addlagatta, A]]	+
-	~~[[Category: Aminopeptidase n]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Metalloprotease]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Thermolysin]]~~	+
-	~~[[Category: Trptophan~~]]	+

OCA at 11:22, 5 January 2022

2022-01-05T11:22:27Z

←Older revision		Revision as of 11:22, 5 January 2022
Line 1:		Line 1:

	==Crystal structure of E. coli Aminopeptidase N in complex with tryptophan==		==Crystal structure of E. coli Aminopeptidase N in complex with tryptophan==
-	<StructureSection load='3b3b' size='340' side='right' caption='[[3b3b]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='3b3b' size='340' side='right'caption='[[3b3b]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b3b]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3B3B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b3b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B3B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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">[[3b2p\|3b2p]], [[2hpo\|2hpo]], [[2hpt\|2hpt]], [[3b2x\|3b2x]], [[3b34\|3b34]], [[3b37\|3b37]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3b2p\|3b2p]], [[2hpo\|2hpo]], [[2hpt\|2hpt]], [[3b2x\|3b2x]], [[3b34\|3b34]], [[3b37\|3b37]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Aminopeptidase N ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Aminopeptidase N ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </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=3b3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3b OCA], [~~http~~://pdbe.org/3b3b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3b3b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3b3b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3b3b 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=3b3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3b OCA], [https://pdbe.org/3b3b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b3b RCSB], [https://www.ebi.ac.uk/pdbsum/3b3b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b3b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AMPN_ECOLI AMPN_ECOLI]] Aminopeptidase N is involved in the degradation of intracellular peptides generated by protein breakdown during normal growth as well as in response to nutrient starvation.	+	[[https://www.uniprot.org/uniprot/AMPN_ECOLI AMPN_ECOLI]] Aminopeptidase N is involved in the degradation of intracellular peptides generated by protein breakdown during normal growth as well as in response to nutrient starvation.
	== 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==
-	*[[Aminopeptidase\|Aminopeptidase]]	+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Membrane alanyl aminopeptidase]]		[[Category: Membrane alanyl aminopeptidase]]
	[[Category: Addlagatta, A]]		[[Category: Addlagatta, A]]

OCA at 08:03, 31 October 2018

2018-10-31T08:03:37Z

←Older revision		Revision as of 08:03, 31 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of E. coli Aminopeptidase N in complex with tryptophan==		==Crystal structure of E. coli Aminopeptidase N in complex with tryptophan==
	<StructureSection load='3b3b' size='340' side='right' caption='[[3b3b]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3b3b' size='340' side='right' caption='[[3b3b]], [[Resolution\|resolution]] 1.85Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Aminopeptidase N ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Aminopeptidase N ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </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=3b3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3b OCA], [http://pdbe.org/3b3b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b3b RCSB], [http://www.ebi.ac.uk/pdbsum/3b3b 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=3b3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3b OCA], [http://pdbe.org/3b3b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b3b RCSB], [http://www.ebi.ac.uk/pdbsum/3b3b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b3b 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/b3/3b3b_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b3/3b3b_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 04:32, 8 February 2016

2016-02-08T04:32:54Z

←Older revision		Revision as of 04:32, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3b3b' size='340' side='right' caption='[[3b3b]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3b3b' size='340' side='right' caption='[[3b3b]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b3b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B3B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b3b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B3B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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">[[3b2p\|3b2p]], [[2hpo\|2hpo]], [[2hpt\|2hpt]], [[3b2x\|3b2x]], [[3b34\|3b34]], [[3b37\|3b37]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b2p\|3b2p]], [[2hpo\|2hpo]], [[2hpt\|2hpt]], [[3b2x\|3b2x]], [[3b34\|3b34]], [[3b37\|3b37]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Aminopeptidase N ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Aminopeptidase N ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </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=3b3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b3b RCSB], [http://www.ebi.ac.uk/pdbsum/3b3b 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=3b3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3b OCA], [http://pdbe.org/3b3b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b3b RCSB], [http://www.ebi.ac.uk/pdbsum/3b3b 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=3b3b 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 3b3b" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli k-12~~]]	+	[[Category: Ecoli]]
	[[Category: Membrane alanyl aminopeptidase]]		[[Category: Membrane alanyl aminopeptidase]]
	[[Category: Addlagatta, A]]		[[Category: Addlagatta, A]]

OCA at 20:38, 24 December 2014

2014-12-24T20:38:46Z

←Older revision		Revision as of 20:38, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3b3b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B3B FirstGlance]. <br>		<table><tr><td colspan='2'>[[3b3b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B3B FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b2p\|3b2p]], [[2hpo\|2hpo]], [[2hpt\|2hpt]], [[3b2x\|3b2x]], [[3b34\|3b34]], [[3b37\|3b37]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b2p\|3b2p]], [[2hpo\|2hpo]], [[2hpt\|2hpt]], [[3b2x\|3b2x]], [[3b34\|3b34]], [[3b37\|3b37]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Aminopeptidase N ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Aminopeptidase N ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </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=3b3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b3b RCSB], [http://www.ebi.ac.uk/pdbsum/3b3b 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=3b3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b3b RCSB], [http://www.ebi.ac.uk/pdbsum/3b3b PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AMPN_ECOLI AMPN_ECOLI]] Aminopeptidase N is involved in the degradation of intracellular peptides generated by protein breakdown during normal growth as well as in response to nutrient starvation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Membrane alanyl aminopeptidase]]		[[Category: Membrane alanyl aminopeptidase]]
-	[[Category: Addlagatta, A.]]	+	[[Category: Addlagatta, A]]
	[[Category: Aminopeptidase n]]		[[Category: Aminopeptidase n]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 07:52, 29 September 2014

2014-09-29T07:52:49Z

←Older revision		Revision as of 07:52, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3b3b.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of E. coli Aminopeptidase N in complex with tryptophan==
		+	<StructureSection load='3b3b' size='340' side='right' caption='[[3b3b]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3b3b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B3B FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b2p\|3b2p]], [[2hpo\|2hpo]], [[2hpt\|2hpt]], [[3b2x\|3b2x]], [[3b34\|3b34]], [[3b37\|3b37]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Aminopeptidase N ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </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=3b3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b3b RCSB], [http://www.ebi.ac.uk/pdbsum/3b3b 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/b3/3b3b_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 ==
		+	Aminopeptidase N from Escherichia coli is a M1 class aminopeptidase with the active-site region related to that of thermolysin. The enzyme has unusual specificity, cleaving adjacent to the large, nonpolar amino acids Phe and Tyr but also cleaving next to the polar residues Lys and Arg. To try to understand the structural basis for this pattern of hydrolysis, the structure of the enzyme was determined in complex with the amino acids l-arginine, l-lysine, l-phenylalanine, l-tryptophan, and l-tyrosine. These amino acids all bind with their backbone atoms close to the active-site zinc ion and their side chain occupying the S1 subsite. This subsite is in the form of a cylinder, about 10 A in cross-section and 12 A in length. The bottom of the cylinder includes the zinc ion and a number of polar side chains that make multiple hydrogen-bonding and other interactions with the alpha-amino group and the alpha-carboxylate of the bound amino acid. The walls of the S1 cylinder are hydrophobic and accommodate the nonpolar or largely nonpolar side chains of Phe and Tyr. The top of the cylinder is polar in character and includes bound water molecules. The epsilon-amino group of the bound lysine side chain and the guanidinium group of arginine both make multiple hydrogen bonds to this part of the S1 site. At the same time, the hydrocarbon part of the lysine and arginine side chains is accommodated within the nonpolar walls of the S1 cylinder. This combination of hydrophobic and hydrophilic binding surfaces explains the ability of ePepN to cleave Lys, Arg, Phe, and Tyr. Another favored substrate has Ala at the P1 position. The short, nonpolar side chain of this residue can clearly be bound within the hydrophobic part of the S1 cylinder, but the reason for its facile hydrolysis remains uncertain.

-	~~{{STRUCTURE_3b3b\| PDB=3b3b \| SCENE= }}~~	+	Structural Basis for the Unusual Specificity of Escherichia coli Aminopeptidase N.,Addlagatta A, Gay L, Matthews BW Biochemistry. 2008 Apr 17;. PMID:18416562<ref>PMID:18416562</ref>

-	~~===Crystal structure~~ of E. ~~coli Aminopeptidase N in complex with tryptophan===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18416562}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3b3b]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA].~~	+

	==See Also==		==See Also==
	*[[Aminopeptidase\|Aminopeptidase]]		*[[Aminopeptidase\|Aminopeptidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018416562<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Membrane alanyl aminopeptidase]]		[[Category: Membrane alanyl aminopeptidase]]

OCA at 08:55, 20 October 2012

2012-10-20T08:55:31Z

←Older revision		Revision as of 08:55, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3b3b]] is a 1 chain structure ~~of [[Aminopeptidase]]~~ with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k12~~ Escherichia coli ~~k12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA].	+	[[3b3b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA].

	==See Also==		==See Also==
Line 15:		Line 15:
	==Reference==		==Reference==
	<ref group="xtra">PMID:018416562</ref><references group="xtra"/>		<ref group="xtra">PMID:018416562</ref><references group="xtra"/>
-	[[Category: Escherichia coli ~~k12~~]]	+	[[Category: Escherichia coli k-12]]
	[[Category: Membrane alanyl aminopeptidase]]		[[Category: Membrane alanyl aminopeptidase]]
	[[Category: Addlagatta, A.]]		[[Category: Addlagatta, A.]]

OCA: Protected "3b3b" [edit=sysop:move=sysop]

2012-07-25T21:12:30Z

Protected "3b3b" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:12, 25 July 2012

OCA at 21:12, 25 July 2012

2012-07-25T21:12:28Z

←Older revision		Revision as of 21:12, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3b3b.png\|left\|200px]]		[[Image:3b3b.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3b3b", 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_3b3b\| PDB=3b3b \| SCENE= }}		{{STRUCTURE_3b3b\| PDB=3b3b \| SCENE= }}

	===Crystal structure of E. coli Aminopeptidase N in complex with tryptophan===		===Crystal structure of E. coli Aminopeptidase N in complex with tryptophan===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18416562}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18416562 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18416562}}		{{ABSTRACT_PUBMED_18416562}}

	==About this Structure==		==About this Structure==
-	~~3B3B~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA].	+	[[3b3b]] is a 1 chain structure of [[Aminopeptidase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA].
		+
		+	==See Also==
		+	*[[Aminopeptidase\|Aminopeptidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18416562~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018416562</ref><references group="xtra"/>
	[[Category: Escherichia coli k12]]		[[Category: Escherichia coli k12]]
	[[Category: Membrane alanyl aminopeptidase]]		[[Category: Membrane alanyl aminopeptidase]]
Line 35:		Line 26:
	[[Category: Thermolysin]]		[[Category: Thermolysin]]
	[[Category: Trptophan]]		[[Category: Trptophan]]
-	[[Category: Zinc]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:50:05 2009''

OCA at 16:50, 16 February 2009

2009-02-16T16:50:08Z

←Older revision		Revision as of 16:50, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3B3B is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA].	+	3B3B is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3B OCA].

	==Reference==		==Reference==
-	~~Structural Basis for the Unusual Specificity of Escherichia coli Aminopeptidase N., Addlagatta A, Gay L, Matthews BW, Biochemistry. 2008 Apr 17;.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18416562 18416562]~~	+	<ref group="xtra">PMID:18416562</ref><references group="xtra"/>
	[[Category: Escherichia coli k12]]		[[Category: Escherichia coli k12]]
	[[Category: Membrane alanyl aminopeptidase]]		[[Category: Membrane alanyl aminopeptidase]]
-	[[Category: Single protein]]
	[[Category: Addlagatta, A.]]		[[Category: Addlagatta, A.]]
	[[Category: Aminopeptidase n]]		[[Category: Aminopeptidase n]]
Line 38:		Line 37:
	[[Category: Zinc]]		[[Category: Zinc]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 2 21~~:58:~~34 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:50:05 2009''