3ckm: Difference between revisions

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-==Crystal Structure of the YraM (LpoA) C-terminal domain==
-<StructureSection load='3ckm' size='340' side='right' caption='[[3ckm]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
+==LpoA (YraM) C-domain from Haemophilus influenzae, a regulator of PBP1A==
+<StructureSection load='3ckm' size='340' side='right'caption='[[3ckm]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ckm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2h4a 2h4a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CKM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ckm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haein Haein]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2h4a 2h4a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CKM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2h4a|2h4a]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5kcn|5kcn]], [[5vat|5vat]], [[5vbg|5vbg]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YraM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YraM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</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=3ckm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ckm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ckm RCSB], [http://www.ebi.ac.uk/pdbsum/3ckm 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=3ckm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ckm OCA], [https://pdbe.org/3ckm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ckm RCSB], [https://www.ebi.ac.uk/pdbsum/3ckm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ckm ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Y1655_HAEIN Y1655_HAEIN]] Regulator of peptidoglycan synthesis that is essential for the function of penicillin-binding protein 1A (PBP1a) (By similarity).[HAMAP-Rule:MF_01890]
+[[https://www.uniprot.org/uniprot/LPOA_HAEIN LPOA_HAEIN]] Regulator of peptidoglycan synthesis that is essential for the function of penicillin-binding protein 1A (PBP1a).
 == 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/ck/3ckm_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ck/3ckm_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=3ckm ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 30: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3ckm" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Haemophilus influenzae]]
+[[Category: Haein]]
+[[Category: Large Structures]]
 [[Category: Saper, M A]]
 [[Category: Vijayalakshmi, J]]
 [[Category: Biosynthetic protein]]
 [[Category: Lipoprotein]]
+[[Category: Pbp1a]]
+[[Category: Peptidoglycan]]
 [[Category: Periplasmic-binding protein]]
+[[Category: Transpeptidase]]
 [[Category: Unliganded]]
 [[Category: Yram]]