2d4r: Difference between revisions

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-{{Seed}}
-[[Image:2d4r.png|left|200px]]
-<!--
+==Crystal structure of TTHA0849 from Thermus thermophilus HB8==
-The line below this paragraph, containing "STRUCTURE_2d4r", creates the "Structure Box" on the page.
+<StructureSection load='2d4r' size='340' side='right'caption='[[2d4r]], [[Resolution|resolution]] 2.40&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'>[[2d4r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4R 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]] 2.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2d4r|  PDB=2d4r  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4r OCA], [https://pdbe.org/2d4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4r RCSB], [https://www.ebi.ac.uk/pdbsum/2d4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4r ProSAT], [https://www.topsan.org/Proteins/RSGI/2d4r TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5SK03_THET8 Q5SK03_THET8]
+== 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/d4/2d4r_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2d4r ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, has been determined at 2.4 A resolution as a part of a structural and functional genomics project on T. thermophilus HB8. The main-chain folding shows a compact alpha+beta motif, forming a hydrophobic cavity in the molecule. A structural similarity search reveals that it resembles those steroidogenic acute regulatory proteins that contain the lipid-transfer (START) domain, even though TTHA0849 shows comparatively weak sequence identity to polyketide cyclases. However, the size of the ligand-binding cavity is distinctly smaller than other START domain-containing proteins, suggesting that it catalyses the transfer of smaller ligand molecules.
-===Crystal structure of TTHA0849 from Thermus thermophilus HB8===
+Structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, at 2.4 A resolution: a putative member of the StAR-related lipid-transfer (START) domain superfamily.,Nakabayashi M, Shibata N, Komori H, Ueda Y, Iino H, Ebihara A, Kuramitsu S, Higuchi Y Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Dec 1;61(Pt, 12):1027-31. Epub 2005 Nov 5. PMID:16511226<ref>PMID:16511226</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_16511226}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2d4r" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16511226 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16511226}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-D4R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4R OCA].
+[[Category: Thermus thermophilus HB8]]
+[[Category: Higuchi Y]]
-==Reference==
+[[Category: Kuramitsu S]]
-Structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, at 2.4 A resolution: a putative member of the StAR-related lipid-transfer (START) domain superfamily., Nakabayashi M, Shibata N, Komori H, Ueda Y, Iino H, Ebihara A, Kuramitsu S, Higuchi Y, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Dec 1;61(Pt, 12):1027-31. Epub 2005 Nov 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16511226 16511226]
+[[Category: Nakabayashi M]]
-[[Category: Single protein]]
+[[Category: Shibata N]]
-[[Category: Thermus thermophilus]]
-[[Category: Higuchi, Y.]]
-[[Category: Kuramitsu, S.]]
-[[Category: Nakabayashi, M.]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
-[[Category: Shibata, N.]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Start domain]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 02:45:40 2008''