1bm1: Difference between revisions

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OCA

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 ==CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN THE LIGHT-ADAPTED STATE==
-<StructureSection load='1bm1' size='340' side='right' caption='[[1bm1]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+<StructureSection load='1bm1' size='340' side='right'caption='[[1bm1]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1bm1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BM1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1bm1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BM1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPG:PHOSPHORIC+ACID+2,3-BIS-(3,7,11,15-TETRAMETHYL-HEXADECYLOXY)-PROPYL+ESTER+2-HYDROXO-3-PHOSPHONOOXY-PROPYL+ESTER'>DPG</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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]] 3.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DPG:PHOSPHORIC+ACID+2,3-BIS-(3,7,11,15-TETRAMETHYL-HEXADECYLOXY)-PROPYL+ESTER+2-HYDROXO-3-PHOSPHONOOXY-PROPYL+ESTER'>DPG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></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=1bm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bm1 OCA], [http://pdbe.org/1bm1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bm1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bm1 PDBsum]</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=1bm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bm1 OCA], [https://pdbe.org/1bm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bm1 RCSB], [https://www.ebi.ac.uk/pdbsum/1bm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bm1 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.
+[https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA] Light-driven proton pump.
 == 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/bm/1bm1_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/1bm1_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].
+</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=1bm1 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / Line 31: @@
 ==See Also==
-*[[Bacteriorhodopsin|Bacteriorhodopsin]]
+*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
 == References ==
 <references/>
@@ Line 36: / Line 37: @@
 </StructureSection>
 [[Category: Halobacterium salinarum]]
-[[Category: Hino, T]]
+[[Category: Large Structures]]
-[[Category: Kamiya, N]]
+[[Category: Hino T]]
-[[Category: Kouyama, T]]
+[[Category: Kamiya N]]
-[[Category: Nakasako, M]]
+[[Category: Kouyama T]]
-[[Category: Okada, T]]
+[[Category: Nakasako M]]
-[[Category: Sato, H]]
+[[Category: Okada T]]
-[[Category: Takeda, K]]
+[[Category: Sato H]]
-[[Category: Tani, K]]
+[[Category: Takeda K]]
-[[Category: Membrane protein]]
+[[Category: Tani K]]
-[[Category: Photoreceptor]]
-[[Category: Proton pump]]
-[[Category: Retinal protein]]