2joo: Difference between revisions

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-[[Image:2joo.png|left|200px]]
-<!--
+==The NMR Solution Structure of Recombinant RGD-hirudin==
-The line below this paragraph, containing "STRUCTURE_2joo", creates the "Structure Box" on the page.
+<StructureSection load='2joo' size='340' side='right'caption='[[2joo]]' 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'>[[2joo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hirudo_medicinalis Hirudo medicinalis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JOO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JOO 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">Solution NMR, 20 models</td></tr>
--->
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2joo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2joo OCA], [https://pdbe.org/2joo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2joo RCSB], [https://www.ebi.ac.uk/pdbsum/2joo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2joo ProSAT]</span></td></tr>
-{{STRUCTURE_2joo|  PDB=2joo  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HIRV1_HIRME HIRV1_HIRME] Hirudin is a potent thrombin-specific protease inhibitor. It forms a stable non-covalent complex with alpha-thrombin, thereby abolishing its ability to cleave fibrinogen.<ref>PMID:17585879</ref>
+== 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/jo/2joo_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=2joo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The solution structure of a new recombinant RGD-hirudin, which has the activities of anti-thrombin and anti-platelet aggregation, was determined by (1)H nuclear magnetic resonance spectroscopy and compared with the conformations of recombinant wild-type hirudin and hirudin (variant 2, Lys47) of the hirudin thrombin complex. On the basis of total 1284 distance and dihedral angle constraints derived from a series of NMR spectra, 20 conformers were computed with ARIA/CNS programs. The structure of residues 3-30 and 37-48 form a molecular core with two antiparallel beta-sheets as the other two hirudins. However, significant differences were found in the surface electrostatic charge distributions among the three hirudins, especially in the RGD segment of recombinant RGD-hirudin. This difference may be greatly beneficial to its additional function of anti-platelet aggregation. The difference in extended C-terminal makes its both ionic and hydrophobic interactions with the fibrinogen recognition exosite of thrombin more effective.
-===The NMR Solution Structure of Recombinant RGD-hirudin===
+The NMR solution structure of recombinant RGD-hirudin.,Song X, Mo W, Liu X, Zhu L, Yan X, Song H, Dai L Biochem Biophys Res Commun. 2007 Aug 17;360(1):103-8. Epub 2007 Jun 13. PMID:17585879<ref>PMID:17585879</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_17585879}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2joo" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17585879 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_17585879}}
-==About this Structure==
-[[2joo]] is a 1 chain structure of [[Hirudin]] with sequence from [http://en.wikipedia.org/wiki/Hirudo_medicinalis Hirudo medicinalis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JOO OCA].
 ==See Also==
-*[[Hirudin]]
+*[[Hirudin 3D structures|Hirudin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:17585879</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Hirudo medicinalis]]
-[[Category: Dai, L.]]
+[[Category: Large Structures]]
-[[Category: Liu, X.]]
+[[Category: Dai L]]
-[[Category: Mo, W.]]
+[[Category: Liu X]]
-[[Category: Song, H.]]
+[[Category: Mo W]]
-[[Category: Song, X.]]
+[[Category: Song H]]
-[[Category: Yan, X.]]
+[[Category: Song X]]
-[[Category: Blood clotting]]
+[[Category: Yan X]]
-[[Category: Mainly beta]]