2d3t: Difference between revisions

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-{{Seed}}
-[[Image:2d3t.png|left|200px]]
-<!--
+==Fatty Acid beta-oxidation multienzyme complex from Pseudomonas Fragi, Form V==
-The line below this paragraph, containing "STRUCTURE_2d3t", creates the "Structure Box" on the page.
+<StructureSection load='2d3t' size='340' side='right'caption='[[2d3t]], [[Resolution|resolution]] 3.40&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'>[[2d3t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3T 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]] 3.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-{{STRUCTURE_2d3t|  PDB=2d3t  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3t OCA], [https://pdbe.org/2d3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3t RCSB], [https://www.ebi.ac.uk/pdbsum/2d3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FADB_PSEFR FADB_PSEFR] Involved in the aerobic and anaerobic degradation of long-chain fatty acids via beta-oxidation cycle. Catalyzes the formation of 3-oxoacyl-CoA from enoyl-CoA via L-3-hydroxyacyl-CoA. It can also use D-3-hydroxyacyl-CoA and cis-3-enoyl-CoA as substrate.[HAMAP-Rule:MF_01621]
+== 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/d3/2d3t_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=2d3t ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The quaternary structure of a fatty acid beta-oxidation multienzyme complex, catalyzing three sequential reactions, was investigated by X-ray crystallographic and small-angle X-ray solution scattering analyses. X-ray crystallography revealed an intermediate structure of the complex among the previously reported structures. However, the theoretical scattering curves calculated from the crystal structures remarkably disagree with the experimental profiles. Instead, an ensemble of the atomic models, which were all calculated by rigid-body optimization, reasonably explained the experimental data. These structures significantly differ from those in the crystals, but they maintain the substrate binding pocket at the domain boundary. Comparisons among these structures indicated that binding of 3-hydroxyhexadecanoyl-CoA or nicotinamide adenine dinucleotide induces domain rearrangements in the complex. The conformational changes suggest the structural events occurring during the chain reaction catalyzed by the multienzyme complex.
-===Fatty Acid beta-oxidation multienzyme complex from Pseudomonas Fragi, Form V===
+Ligand-induced domain rearrangement of fatty acid beta-oxidation multienzyme complex.,Tsuchiya D, Shimizu N, Ishikawa M, Suzuki Y, Morikawa K Structure. 2006 Feb;14(2):237-46. PMID:16472743<ref>PMID:16472743</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2d3t" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16472743}}, adds the Publication Abstract to the page
+*[[Thiolase 3D structures|Thiolase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16472743 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16472743}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-D3T is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3T OCA].
-==Reference==
-<ref group="xtra">PMID:16472743</ref><ref group="xtra">PMID:15229654</ref><references group="xtra"/>
-[[Category: Acetyl-CoA C-acyltransferase]]
 [[Category: Pseudomonas fragi]]
-[[Category: Ishikawa, M.]]
+[[Category: Ishikawa M]]
-[[Category: Morikawa, K.]]
+[[Category: Morikawa K]]
-[[Category: Shimizu, N.]]
+[[Category: Shimizu N]]
-[[Category: Suzuki, Y.]]
+[[Category: Suzuki Y]]
-[[Category: Tsuchiya, D.]]
+[[Category: Tsuchiya D]]
-[[Category: Alpha2beta2 heterotetrameric complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:56:36 2009''