2i19: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:2i19.png|left|200px]]
-<!--
+==T. Brucei farnesyl diphosphate synthase complexed with bisphosphonate==
-The line below this paragraph, containing "STRUCTURE_2i19", creates the "Structure Box" on the page.
+<StructureSection load='2i19' size='340' side='right'caption='[[2i19]], [[Resolution|resolution]] 2.28&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'>[[2i19]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I19 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I19 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]] 2.28&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1BY:[2-(PYRIDIN-2-YLAMINO)ETHANE-1,1-DIYL]BIS(PHOSPHONIC+ACID)'>1BY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_2i19|  PDB=2i19  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2i19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i19 OCA], [https://pdbe.org/2i19 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i19 RCSB], [https://www.ebi.ac.uk/pdbsum/2i19 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i19 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q86C09_9TRYP Q86C09_9TRYP]
+== 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/i1/2i19_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=2i19 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bisphosphonates are a class of molecules in widespread use in treating bone resorption diseases and are also of interest as immunomodulators and anti-infectives. They function by inhibiting the enzyme farnesyl diphosphate synthase (FPPS), but the details of how these molecules bind are not fully understood. Here, we report the results of a solid-state (13)C, (15)N, and (31)P magic-angle sample spinning (MAS) NMR and quantum chemical investigation of several bisphosphonates, both as pure compounds and when bound to FPPS, to provide information about side-chain and phosphonate backbone protonation states when bound to the enzyme. We then used computational docking methods (with the charges assigned by NMR) to predict how several bisphosphonates bind to FPPS. Finally, we used X-ray crystallography to determine the structures of two potent bisphosphonate inhibitors, finding good agreement with the computational results, opening up the possibility of using the combination of NMR, quantum chemistry and molecular docking to facilitate the design of other, novel prenytransferase inhibitors.
-===T. Brucei farnesyl diphosphate synthase complexed with bisphosphonate===
+Solid-state NMR, crystallographic, and computational investigation of bisphosphonates and farnesyl diphosphate synthase-bisphosphonate complexes.,Mao J, Mukherjee S, Zhang Y, Cao R, Sanders JM, Song Y, Zhang Y, Meints GA, Gao YG, Mukkamala D, Hudock MP, Oldfield E J Am Chem Soc. 2006 Nov 15;128(45):14485-97. PMID:17090032<ref>PMID:17090032</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17090032}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2i19" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17090032 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_17090032}}
-==About this Structure==
-[[2i19]] is a 2 chain structure of [[Farnesyl diphosphate synthase]] with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I19 OCA].
 ==See Also==
-*[[Farnesyl diphosphate synthase|Farnesyl diphosphate synthase]]
+*[[Farnesyl diphosphate synthase 3D structures|Farnesyl diphosphate synthase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017090032</ref><references group="xtra"/>
+__TOC__
-[[Category: Geranyltranstransferase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Trypanosoma brucei]]
-[[Category: Cao, R.]]
+[[Category: Cao R]]
-[[Category: Gao, Y.]]
+[[Category: Gao Y]]
-[[Category: Goddard, A.]]
+[[Category: Goddard A]]
-[[Category: Mao, J.]]
+[[Category: Mao J]]
-[[Category: Odeh, S.]]
+[[Category: Odeh S]]
-[[Category: Oldfield, E.]]
+[[Category: Oldfield E]]
-[[Category: Robinson, H.]]
+[[Category: Robinson H]]
-[[Category: Protein-bisphosphonate complex]]
-[[Category: Transferase]]