3bec: Difference between revisions

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 ==Crystal structure of E. coli penicillin-binding protein 5 in complex with a peptide-mimetic cephalosporin==
-<StructureSection load='3bec' size='340' side='right' caption='[[3bec]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='3bec' size='340' side='right'caption='[[3bec]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bec]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BEC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BEC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bec]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BEC 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=HJ2:(2R)-2-[(R)-{[(6S)-6-AMINO-6-CARBOXYHEXANOYL]AMINO}(CARBOXY)METHYL]-5-METHYL-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC+ACID'>HJ2</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]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3beb|3beb]]</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=HJ2:(2R)-2-[(R)-{[(6S)-6-AMINO-6-CARBOXYHEXANOYL]AMINO}(CARBOXY)METHYL]-5-METHYL-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC+ACID'>HJ2</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dacA, pfv ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3bec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bec OCA], [https://pdbe.org/3bec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bec RCSB], [https://www.ebi.ac.uk/pdbsum/3bec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bec 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=3bec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bec OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bec RCSB], [http://www.ebi.ac.uk/pdbsum/3bec PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DACA_ECOLI DACA_ECOLI]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
+[https://www.uniprot.org/uniprot/DACA_ECOLI DACA_ECOLI] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
 == 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/be/3bec_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/be/3bec_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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].
+</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=3bec ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3bec" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Penicillin-binding protein|Penicillin-binding protein]]
+*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
 == References ==
 <references/>
@@ Line 36: / Line 37: @@
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Davies, C]]
+[[Category: Large Structures]]
-[[Category: Powell, A J]]
+[[Category: Davies C]]
-[[Category: Cell shape]]
+[[Category: Powell AJ]]
-[[Category: Cell wall biogenesis/degradation]]
-[[Category: Dd-carboxypeptidase]]
-[[Category: Designed cephalosporin]]
-[[Category: Hydrolase]]
-[[Category: Inner membrane]]
-[[Category: Membrane]]
-[[Category: Penicillin-binding protein]]
-[[Category: Peptidoglycan synthesis]]
-[[Category: Protease]]