3d8z: Difference between revisions

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-{{STRUCTURE_3d8z|  PDB=3d8z  |  SCENE=  }}
+==RNase A- 5'-Deoxy-5'-N-pyrrolidinothymidine complex==
-===RNase A- 5'-Deoxy-5'-N-pyrrolidinothymidine complex===
+<StructureSection load='3d8z' size='340' side='right' caption='[[3d8z]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
-{{ABSTRACT_PUBMED_19173562}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3d8z]] is a 2 chain structure with 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=3D8Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D8Z FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3d8y|3d8y]]</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3d8z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d8z RCSB], [http://www.ebi.ac.uk/pdbsum/3d8z PDBsum]</span></td></tr>
+</table>
+== 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/chain_selection.php?pdb_ID=2ata 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.
-==Function==
+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>
-[[http://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>
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[3d8z]] is a 2 chain structure with 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=3D8Z OCA].
+</div>
 ==See Also==
 *[[Ribonuclease|Ribonuclease]]
+*[[Temp|Temp]]
-==Reference==
+*[[User:Jaime.Prilusky/Test/tree|User:Jaime.Prilusky/Test/tree]]
-<ref group="xtra">PMID:019173562</ref><references group="xtra"/><references/>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
 [[Category: Pancreatic ribonuclease]]
-[[Category: Leonidas, D D.]]
+[[Category: Leonidas, D D]]
-[[Category: Oikonomakos, N G.]]
+[[Category: Oikonomakos, N G]]
-[[Category: Zographos, S E.]]
+[[Category: Zographos, S E]]
 [[Category: Endonuclease]]
 [[Category: Glycation]]