1qrk: Difference between revisions

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-{{Seed}}
-[[Image:1qrk.png|left|200px]]
-<!--
+==HUMAN FACTOR XIII WITH STRONTIUM BOUND IN THE ION SITE==
-The line below this paragraph, containing "STRUCTURE_1qrk", creates the "Structure Box" on the page.
+<StructureSection load='1qrk' size='340' side='right'caption='[[1qrk]], [[Resolution|resolution]] 2.50&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'>[[1qrk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1bl2 1bl2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QRK 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
-{{STRUCTURE_1qrk|  PDB=1qrk  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qrk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qrk OCA], [https://pdbe.org/1qrk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qrk RCSB], [https://www.ebi.ac.uk/pdbsum/1qrk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qrk ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/F13A_HUMAN F13A_HUMAN] Defects in F13A1 are the cause of factor XIII subunit A deficiency (FA13AD) [MIM:[https://omim.org/entry/613225 613225]. FA13AD is an autosomal recessive disorder characterized by a life-long bleeding tendency, impaired wound healing and spontaneous abortion in affected women.<ref>PMID:1353995</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/F13A_HUMAN F13A_HUMAN] Factor XIII is activated by thrombin and calcium ion to a transglutaminase that catalyzes the formation of gamma-glutamyl-epsilon-lysine cross-links between fibrin chains, thus stabilizing the fibrin clot. Also cross-link alpha-2-plasmin inhibitor, or fibronectin, to the alpha chains of fibrin.
+== 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/qr/1qrk_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=1qrk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The presence or absence of calcium determines the activation, activity, oligomerization, and stability of blood coagulation factor XIII. To explore these observed effects, we have determined the x-ray crystal structure of recombinant factor XIII A2 in the presence of calcium, strontium, and ytterbium. The main calcium binding site within each monomer involves the main chain oxygen atom of Ala-457, and also the side chains from residues Asn-436, Asp-438, Glu-485, and Glu-490. Calcium and strontium bind in the same location, while ytterbium binds several angstroms removed. A novel ytterbium binding site is also found at the dimer two-fold axis, near residues Asp-270 and Glu-272, and this site may be related to the reported inhibition by lanthanide metals (Achyuthan, K. E., Mary, A., and Greenberg, C. S. (1989) Biochem. J. 257, 331-338). The overall structure of ion-bound factor XIII is very similar to the previously determined crystal structures of factor XIII zymogen, likely due to the constraints of this monoclinic crystal form. We have merged the three independent sets of water molecules in the structures to determine which water molecules are conserved and possibly structurally significant.
-===HUMAN FACTOR XIII WITH STRONTIUM BOUND IN THE ION SITE===
+Identification of the calcium binding site and a novel ytterbium site in blood coagulation factor XIII by x-ray crystallography.,Fox BA, Yee VC, Pedersen LC, Le Trong I, Bishop PD, Stenkamp RE, Teller DC J Biol Chem. 1999 Feb 19;274(8):4917-23. PMID:9988734<ref>PMID:9988734</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1qrk" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9988734}}, adds the Publication Abstract to the page
+*[[Factor XIII|Factor XIII]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9988734 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9988734}}
+__TOC__
+</StructureSection>
-==About this Structure==
-QRK is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1bl2 1bl2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRK OCA].
-==Reference==
-<ref group="xtra">PMID:9988734</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Protein-glutamine gamma-glutamyltransferase]]
+[[Category: Large Structures]]
-[[Category: Bishop, P D.]]
+[[Category: Bishop PD]]
-[[Category: Fox, B A.]]
+[[Category: Fox BA]]
-[[Category: Pederson, L C.]]
+[[Category: Le Trong I]]
-[[Category: Stenkamp, R E.]]
+[[Category: Pederson LC]]
-[[Category: Teller, D C.]]
+[[Category: Stenkamp RE]]
-[[Category: Trong, I Le.]]
+[[Category: Teller DC]]
-[[Category: Yee, V C.]]
+[[Category: Yee VC]]
-[[Category: Blood coagulation]]
-[[Category: Calcium]]
-[[Category: Strontium]]
-[[Category: Transglutaminase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:36:13 2009''