3mb5: Difference between revisions

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 ==Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-methionine==
-<StructureSection load='3mb5' size='340' side='right' caption='[[3mb5]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='3mb5' size='340' side='right'caption='[[3mb5]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3mb5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MB5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MB5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3mb5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MB5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">[[3lga|3lga]], [[3lhd|3lhd]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAB0283, pimT-like, PYRAB04300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</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=3mb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mb5 OCA], [https://pdbe.org/3mb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mb5 RCSB], [https://www.ebi.ac.uk/pdbsum/3mb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mb5 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/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.217, 2.1.1.218, 2.1.1.219 and 2.1.1.220 2.1.1.217, 2.1.1.218, 2.1.1.219 and 2.1.1.220] </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=3mb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mb5 OCA], [http://pdbe.org/3mb5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mb5 RCSB], [http://www.ebi.ac.uk/pdbsum/3mb5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3mb5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TRMI_PYRAB TRMI_PYRAB]] Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenosine at position(s) 57 (m1A57) and 58 (m1A58) in the T-loop of some tRNAs. Methylates the first adenine of an AA sequence.<ref>PMID:14739239</ref> <ref>PMID:20483913</ref>
+[https://www.uniprot.org/uniprot/TRMI_PYRAB TRMI_PYRAB] Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenosine at position(s) 57 (m1A57) and 58 (m1A58) in the T-loop of some tRNAs. Methylates the first adenine of an AA sequence.<ref>PMID:14739239</ref> <ref>PMID:20483913</ref>
 == 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/mb/3mb5_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mb/3mb5_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>
@@ Line 33: / Line 31: @@
 ==See Also==
-*[[SAM-dependent methyltransferase|SAM-dependent methyltransferase]]
+*[[SAM-dependent methyltrasferase 3D structures|SAM-dependent methyltrasferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus abyssi erauso et al. 1993]]
+[[Category: Large Structures]]
-[[Category: Transferase]]
+[[Category: Pyrococcus abyssi]]
-[[Category: Golinelli-Pimpaneau, B]]
+[[Category: Golinelli-Pimpaneau B]]
-[[Category: Guelorget, A]]
+[[Category: Guelorget A]]
-[[Category: Disulfide bond]]
-[[Category: Hyperthermostability]]
-[[Category: Intermolecular contact]]
-[[Category: M1a]]
-[[Category: Methyltransferase]]
-[[Category: Region-specificity]]
-[[Category: Rna methyltransferase]]
-[[Category: Tetramer]]
-[[Category: Trmi]]