2ek9: Difference between revisions

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OCA

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-[[Image:2ek9.jpg|left|200px]]
- {{Structure
+==Aminopeptidase from Aneurinibacillus sp. strain AM-1 with Bestatin==
-|PDB= 2ek9 |SIZE=350|CAPTION= <scene name='initialview01'>2ek9</scene>, resolution 1.97&Aring;
+<StructureSection load='2ek9' size='340' side='right'caption='[[2ek9]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A+1001'>AC1</scene>, <scene name='pdbsite=AC2:Zn+Binding+Site+For+Residue+A+1002'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Residue+A+1003'>AC3</scene>, <scene name='pdbsite=AC4:Zn+Binding+Site+For+Residue+A+1004'>AC4</scene>, <scene name='pdbsite=AC5:Zn+Binding+Site+For+Residue+A+1005'>AC5</scene>, <scene name='pdbsite=AC6:Zn+Binding+Site+For+Residue+A+1006'>AC6</scene>, <scene name='pdbsite=AC7:Bes+Binding+Site+For+Residue+A+2001'>AC7</scene> and <scene name='pdbsite=AC8:Ipa+Binding+Site+For+Residue+A+3001'>AC8</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=BES:2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC+ACID'>BES</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+<table><tr><td colspan='2'>[[2ek9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aneurinibacillus_sp._AM-1 Aneurinibacillus sp. AM-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EK9 FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.97&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BES:2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC+ACID'>BES</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam04389 Peptidase_M28], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd02133 PA_C5a_like]</span>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ek9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ek9 OCA], [https://pdbe.org/2ek9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ek9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ek9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ek9 ProSAT]</span></td></tr>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ek9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ek9 OCA], [http://www.ebi.ac.uk/pdbsum/2ek9 PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2ek9 RCSB]</span>
+</table>
-}}
+== Function ==
+[https://www.uniprot.org/uniprot/A2V759_9BACL A2V759_9BACL]
+== 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/ek/2ek9_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/main_output.php?pdb_ID=2ek9 ConSurf].
+<div style="clear:both"></div>
-'''Aminopeptidase from Aneurinibacillus sp. strain AM-1 with Bestatin'''
+==See Also==
+*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-To elucidate the structure and molecular mechanism of a characteristic proline-specific aminopeptidase produced by the thermophile Aneurinibacillus sp. strain AM-1, its gene was cloned and the recombinant protein was overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 1.8 A resolution from the recombinant aminopeptidase crystal. The crystals belong to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 93.62, b = 68.20, c = 76.84 A. A complete data set was also obtained from crystals of SeMet-substituted aminopeptidase. Data in the resolution range 20-2.1 A from the MAD data set from the SeMet-substituted crystal were used for phase determination.
+[[Category: Aneurinibacillus sp. AM-1]]
+[[Category: Large Structures]]
-==About this Structure==
+[[Category: Akioka M]]
-EK9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EK9 OCA].
+[[Category: Nakano H]]
+[[Category: Watanabe K]]
-==Reference==
-Overexpression, purification, crystallization and preliminary X-ray crystallographic studies of a proline-specific aminopeptidase from Aneurinibacillus sp. strain AM-1., Akioka M, Nakano H, Horikiri A, Tsujimoto Y, Matsui H, Shimizu T, Nakatsu T, Kato H, Watanabe K, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt, 12):1266-8. Epub 2006 Nov 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17142913 17142913]
-[[Category: Bacteria]]
-[[Category: Single protein]]
-[[Category: Akioka, M.]]
-[[Category: Nakano, H.]]
-[[Category: Watanabe, K.]]
-[[Category: hydrolase]]
-[[Category: metalloproteinase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 09:51:01 2008''