3d8z: Difference between revisions

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-{{Seed}}
-[[Image:3d8z.jpg|left|200px]]
-<!--
+==RNase A- 5'-Deoxy-5'-N-pyrrolidinothymidine complex==
-The line below this paragraph, containing "STRUCTURE_3d8z", creates the "Structure Box" on the page.
+<StructureSection load='3d8z' size='340' side='right'caption='[[3d8z]], [[Resolution|resolution]] 1.98&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'>[[3d8z]] 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=3D8Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D8Z 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]] 1.98&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=TXS:1-(2,5-DIDEOXY-5-PYRROLIDIN-1-YL-BETA-L-ERYTHRO-PENTOFURANOSYL)-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE'>TXS</scene></td></tr>
-{{STRUCTURE_3d8z|  PDB=3d8z  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d8z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8z OCA], [https://pdbe.org/3d8z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d8z RCSB], [https://www.ebi.ac.uk/pdbsum/3d8z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8z 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/d8/3d8z_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=3d8z ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Six 5'-deoxy-5'-morpholine, piperidine, and pyrrolidine of pyrimidine nucleosides have been synthesized and characterized. Their inhibitory action to ribonuclease A has been studied by biochemical analysis and X-ray crystallography. These compounds are moderate inhibitors of RNase A with mid-to-upper micromolar inhibition constants (K(i)). The high resolution X-ray crystal structures of the RNase A-inhibitor complexes have shown that all inhibitors bind at the enzyme catalytic cleft with the pyrimidine nucleobase at the B(1)R(2) subsites while the 5' group binds away from the main subsite P(1), where P-O(5') bond cleavage occurs, toward the solvent close to subsite P(0). Structure-activity relationship analysis has demonstrated that the compounds with the larger group in the 5' position are more potent. Comparative structural analysis of these RNase A complexes with other similar RNase A-ligand complexes provides a structural explanation of their potency and suggests ways to improve their efficiency and selectivity. These inhibitors can be the starting point for the development of compounds that can be used as pharmaceuticals against pathologies associated with RNase A homologues such as human angiogenin, which is implicated in tumor induced neovascularization.
-===RNase A- 5'-Deoxy-5'-N-pyrrolidinothymidine complex===
+Morpholino, Piperidino, and Pyrrolidino Derivatives of Pyrimidine Nucleosides as Inhibitors of Ribonuclease A: Synthesis, Biochemical, and Crystallographic Evaluation (#) (,) (dagger).,Samanta A, Leonidas DD, Dasgupta S, Pathak T, Zographos SE, Oikonomakos NG J Med Chem. 2009 Jan 27. PMID:19173562<ref>PMID:19173562</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3d8z" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19173562}}, adds the Publication Abstract to the page
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19173562 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19173562}}
+__TOC__
+</StructureSection>
-==About this Structure==
-D8Z is a 2 chains structure of sequences 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=3D8Z OCA].
-==Reference==
-<ref group="xtra">PMID:19173562</ref><references group="xtra"/>
 [[Category: Bos taurus]]
-[[Category: Pancreatic ribonuclease]]
+[[Category: Large Structures]]
-[[Category: Leonidas, D D.]]
+[[Category: Leonidas DD]]
-[[Category: Oikonomakos, N G.]]
+[[Category: Oikonomakos NG]]
-[[Category: Zographos, S E.]]
+[[Category: Zographos SE]]
-[[Category: Endonuclease]]
-[[Category: Glycation]]
-[[Category: Glycoprotein]]
-[[Category: Hydrolase]]
-[[Category: Ligand binding]]
-[[Category: Nuclease]]
-[[Category: Ribonuclease]]
-[[Category: Secreted]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 11 12:40:42 2009''