3cmd: Difference between revisions

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-{{Seed}}
-[[Image:3cmd.jpg|left|200px]]
-<!--
+==Crystal structure of peptide deformylase from VRE-E.faecium==
-The line below this paragraph, containing "STRUCTURE_3cmd", creates the "Structure Box" on the page.
+<StructureSection load='3cmd' size='340' side='right'caption='[[3cmd]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3cmd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CMD FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_3cmd|  PDB=3cmd  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmd OCA], [https://pdbe.org/3cmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cmd RCSB], [https://www.ebi.ac.uk/pdbsum/3cmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmd ProSAT]</span></td></tr>
+</table>
-===Crystal structure of peptide deformylase from VRE-E.faecium===
+== Function ==
+[https://www.uniprot.org/uniprot/Q842S4_ENTFC Q842S4_ENTFC] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).[HAMAP-Rule:MF_00163]
+== Evolutionary Conservation ==
-==About this Structure==
+[[Image:Consurf_key_small.gif|200px|right]]
-CMD is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CMD OCA].
+Check<jmol>
+  <jmolCheckbox>
-==Reference==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cm/3cmd_consurf.spt"</scriptWhenChecked>
-Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure., Nam KH, Ham JI, Priyadarshi A, Kim EE, Chung N, Hwang KY, Proteins. 2009 Jan;74(1):261-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18831047 18831047]
+    <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=3cmd ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
 [[Category: Enterococcus faecium]]
-[[Category: Peptide deformylase]]
+[[Category: Large Structures]]
-[[Category: Hwang, K Y.]]
+[[Category: Hwang KY]]
-[[Category: Nam, K H.]]
+[[Category: Nam KH]]
-[[Category: Hydrolase]]
-[[Category: Pdf]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 14 13:17:58 2009''