1odf: Difference between revisions

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-{{Seed}}
-[[Image:1odf.png|left|200px]]
-<!--
+==Structure of YGR205w protein.==
-The line below this paragraph, containing "STRUCTURE_1odf", creates the "Structure Box" on the page.
+<StructureSection load='1odf' size='340' side='right'caption='[[1odf]], [[Resolution|resolution]] 2.25&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'>[[1odf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ODF 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]] 2.25&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1odf|  PDB=1odf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1odf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1odf OCA], [https://pdbe.org/1odf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1odf RCSB], [https://www.ebi.ac.uk/pdbsum/1odf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1odf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TDA10_YEAST TDA10_YEAST] ATP-dependent kinase whose specificity is not yet known.
+== 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/od/1odf_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=1odf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The protein product of the YGR205w gene of Saccharomyces cerevisiae was targeted as part of our yeast structural genomics project. YGR205w codes for a small (290 amino acids) protein with unknown structure and function. The only recognizable sequence feature is the presence of a Walker A motif (P loop) indicating a possible nucleotide binding/converting function. We determined the three-dimensional crystal structure of Se-methionine substituted protein using multiple anomalous diffraction. The structure revealed a well known mononucleotide fold and strong resemblance to the structure of small metabolite phosphorylating enzymes such as pantothenate and phosphoribulo kinase. Biochemical experiments show that YGR205w binds specifically ATP and, less tightly, ADP. The structure also revealed the presence of two bound sulphate ions, occupying opposite niches in a canyon that corresponds to the active site of the protein. One sulphate is bound to the P-loop in a position that corresponds to the position of beta-phosphate in mononucleotide protein ATP complex, suggesting the protein is indeed a kinase. The nature of the phosphate accepting substrate remains to be determined.
-===STRUCTURE OF YGR205W PROTEIN.===
+Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase.,de La Sierra-Gallay IL, Collinet B, Graille M, Quevillon-Cheruel S, Liger D, Minard P, Blondeau K, Henckes G, Aufrere R, Leulliot N, Zhou CZ, Sorel I, Ferrer JL, Poupon A, Janin J, van Tilbeurgh H Proteins. 2004 Mar 1;54(4):776-83. PMID:14997573<ref>PMID:14997573</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_14997573}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1odf" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 14997573 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14997573}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-ODF is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODF OCA].
-==Reference==
-<ref group="xtra">PMID:14997573</ref><references group="xtra"/>
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Sierra-Gallay, I Li De La.]]
+[[Category: Li De La Sierra-Gallay I]]
-[[Category: Tilbeurgh, H Van.]]
+[[Category: Van Tilbeurgh H]]
-[[Category: Atp binding protein]]
-[[Category: Yeast protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:08:50 2009''