1pcw: Difference between revisions

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-{{Seed}}
-[[Image:1pcw.png|left|200px]]
-<!--
+==Aquifex aeolicus KDO8PS in complex with cadmium and APP, a bisubstrate inhibitor==
-The line below this paragraph, containing "STRUCTURE_1pcw", creates the "Structure Box" on the page.
+<StructureSection load='1pcw' size='340' side='right'caption='[[1pcw]], [[Resolution|resolution]] 1.85&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'>[[1pcw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PCW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PCW 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]] 1.85&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=H4P:1-DEOXY-6-O-PHOSPHONO-1-[(PHOSPHONOMETHYL)AMINO]-L-THREO-HEXITOL'>H4P</scene></td></tr>
-{{STRUCTURE_1pcw|  PDB=1pcw  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pcw OCA], [https://pdbe.org/1pcw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pcw RCSB], [https://www.ebi.ac.uk/pdbsum/1pcw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pcw ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KDSA_AQUAE KDSA_AQUAE]
+== 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/pc/1pcw_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/main_output.php?pdb_ID=1pcw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+-Deoxy-D-manno-octulosonate 8-phosphate (KDO8P) is the phosphorylated precursor of KDO, an essential sugar of the lipopolysaccharide of Gram negative bacteria. KDO8P is produced by a specific synthase (KDO8PS) by condensing arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP), with release of inorganic phosphate. As KDO8PS is present in bacteria and plants, but not in mammalian cells, and mutations that inactivate KDO8PS also block cell replication, KDO8PS is a promising target for the design of new antimicrobials that act by blocking lipopolysaccharide biosynthesis. Previous studies have shown that a compound mimicking an intermediate of the condensation reaction is a good ligand and a powerful inhibitor. Here we report on the crystallographic investigation of the binding to KDO8PS of new derivatives of this original inhibitor. The structures of the enzyme in complex with these compounds, and also with the PEP analogs, 2-phosphoglyceric acid (2-PGA) and Z-methyl-PEP, point to future strategies for the design of novel inhibitors of KDO8PS.
-===Aquifex aeolicus KDO8PS in complex with cadmium and APP, a bisubstrate inhibitor===
+Structure-based design of novel inhibitors of 3-deoxy-D-manno-octulosonate 8-phosphate synthase.,Xu X, Wang J, Grison C, Petek S, Coutrot P, Birck MR, Woodard RW, Gatti DL Drug Des Discov. 2003;18(2-3):91-9. PMID:14675946<ref>PMID:14675946</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1pcw" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14675946}}, adds the Publication Abstract to the page
+*[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14675946 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14675946}}
+__TOC__
+</StructureSection>
-==About this Structure==
-PCW is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PCW OCA].
-==Reference==
-<ref group="xtra">PMID:14675946</ref><references group="xtra"/>
-[[Category: 3-deoxy-8-phosphooctulonate synthase]]
 [[Category: Aquifex aeolicus]]
-[[Category: Birck, M.]]
+[[Category: Large Structures]]
-[[Category: Coutrot, P.]]
+[[Category: Birck M]]
-[[Category: Gatti, D L.]]
+[[Category: Coutrot P]]
-[[Category: Grison, C.]]
+[[Category: Gatti DL]]
-[[Category: Petek, S.]]
+[[Category: Grison C]]
-[[Category: Wang, J.]]
+[[Category: Petek S]]
-[[Category: Woodard, R W.]]
+[[Category: Wang J]]
-[[Category: Xu, X.]]
+[[Category: Woodard RW]]
-[[Category: Lyase]]
+[[Category: Xu X]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 10:10:53 2009''