1z6d: Difference between revisions

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-{{Seed}}
-[[Image:1z6d.png|left|200px]]
-<!--
+==Ribonuclease A- IMP complex==
-The line below this paragraph, containing "STRUCTURE_1z6d", creates the "Structure Box" on the page.
+<StructureSection load='1z6d' size='340' side='right'caption='[[1z6d]], [[Resolution|resolution]] 1.54&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'>[[1z6d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z6D 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]] 1.54&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene></td></tr>
-{{STRUCTURE_1z6d|  PDB=1z6d  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1z6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z6d OCA], [https://pdbe.org/1z6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z6d RCSB], [https://www.ebi.ac.uk/pdbsum/1z6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z6d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</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/z6/1z6d_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=1z6d ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The binding of inosine 5' phosphate (IMP) to ribonuclease A has been studied by kinetic and X-ray crystallographic experiments at high (1.5 A) resolution. IMP is a competitive inhibitor of the enzyme with respect to C&gt;p and binds to the catalytic cleft by anchoring three IMP molecules in a novel binding mode. The three IMP molecules are connected to each other by hydrogen bond and van der Waals interactions and collectively occupy the B1R1P1B2P0P(-1) region of the ribonucleolytic active site. One of the IMP molecules binds with its nucleobase in the outskirts of the B2 subsite and interacts with Glu111 while its phosphoryl group binds in P1. Another IMP molecule binds by following the retro-binding mode previously observed only for guanosines with its nucleobase at B1 and the phosphoryl group in P(-1). The third IMP molecule binds in a novel mode towards the C-terminus. The RNase A-IMP complex provides structural evidence for the functional components of subsite P(-1) while it further supports the role inferred by other studies to Asn71 as the primary structural determinant for the adenine specificity of the B2 subsite. Comparative structural analysis of the IMP and AMP complexes highlights key aspects of the specificity of the base binding subsites of RNase A and provides a structural explanation for their potencies. The binding of IMP suggests ways to develop more potent inhibitors of the pancreatic RNase superfamily using this nucleotide as the starting point.
-===Ribonuclease A- IMP complex===
+The binding of IMP to ribonuclease A.,Hatzopoulos GN, Leonidas DD, Kardakaris R, Kobe J, Oikonomakos NG FEBS J. 2005 Aug;272(15):3988-4001. PMID:16045769<ref>PMID:16045769</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1z6d" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16045769}}, adds the Publication Abstract to the page
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16045769 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16045769}}
+__TOC__
+</StructureSection>
-==About this Structure==
-Z6D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z6D OCA].
-==Reference==
-The binding of IMP to ribonuclease A., Hatzopoulos GN, Leonidas DD, Kardakaris R, Kobe J, Oikonomakos NG, FEBS J. 2005 Aug;272(15):3988-4001. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16045769 16045769]
 [[Category: Bos taurus]]
-[[Category: Pancreatic ribonuclease]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Hatzopoulos GN]]
-[[Category: Hatzopoulos, G N.]]
+[[Category: Kardakaris R]]
-[[Category: Kardakaris, R.]]
+[[Category: Kobe J]]
-[[Category: Kobe, J.]]
+[[Category: Leonidas DD]]
-[[Category: Leonidas, D D.]]
+[[Category: Oikonomakos NG]]
-[[Category: Oikonomakos, N G.]]
-[[Category: Hydrolase]]
-[[Category: Ribonuclease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 12:53:36 2008''