3ghr: Difference between revisions

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-{{Seed}}
-[[Image:3ghr.png|left|200px]]
-<!--
+==Human aldose reductase in complex with NADP+ and the inhibitor IDD594. Investigation of global effects of radiation damage on protein structure. First stage of radiation damage==
-The line below this paragraph, containing "STRUCTURE_3ghr", creates the "Structure Box" on the page.
+<StructureSection load='3ghr' size='340' side='right'caption='[[3ghr]], [[Resolution|resolution]] 1.00&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'>[[3ghr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GHR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GHR 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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=LDT:IDD594'>LDT</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
-{{STRUCTURE_3ghr|  PDB=3ghr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ghr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ghr OCA], [https://pdbe.org/3ghr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ghr RCSB], [https://www.ebi.ac.uk/pdbsum/3ghr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ghr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ALDR_HUMAN ALDR_HUMAN] Catalyzes the NADPH-dependent reduction of a wide variety of carbonyl-containing compounds to their corresponding alcohols with a broad range of catalytic efficiencies.
+== 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/gh/3ghr_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=3ghr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+X-rays interact with biological matter and cause damage. Proteins and other macromolecules are damaged primarily by ionizing X-ray photons and secondarily by reactive radiolytic chemical species. In particular, protein molecules are damaged during X-ray diffraction experiments with protein crystals, which is, in many cases, a serious hindrance to structure solution. The local X-ray-induced structural changes of the protein molecule have been studied using a number of model systems. However, it is still not well understood whether these local chemical changes lead to global structural changes in protein and what the mechanism is. We present experimental evidence at atomic resolution indicating the movement of large parts of the protein globule together with bound water molecules in the early stages of radiation damage to the protein crystal. The data were obtained from a crystal cryocooled to approximately 100 K and diffracting to 1 A. The movement of the protein structural elements occurs simultaneously with the decarboxylation of several glutamate and aspartate residues that mediate contacts between moving protein structural elements and with the rearrangement of the water network. The analysis of the anisotropy of atomic displacement parameters reveals that the observed atomic movements occur at different rates in different unit cells of the crystal. Thus, the examination of the cooperative atomic movement enables us to better understand how radiation-induced local chemical and structural changes of the protein molecule eventually lead to disorder in protein crystals.
-===Human aldose reductase in complex with NADP+ and the inhibitor IDD594. Investigation of global effects of radiation damage on protein structure. First stage of radiation damage===
+X-ray-radiation-induced cooperative atomic movements in protein.,Petrova T, Lunin VY, Ginell S, Hazemann I, Lazarski K, Mitschler A, Podjarny A, Joachimiak A J Mol Biol. 2009 Apr 17;387(5):1092-105. Epub 2009 Feb 20. PMID:19233199<ref>PMID:19233199</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ghr" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19233199}}, adds the Publication Abstract to the page
+*[[Aldose reductase 3D structures|Aldose reductase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19233199 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19233199}}
+__TOC__
+</StructureSection>
-==About this Structure==
-GHR is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GHR OCA].
-==Reference==
-<ref group="xtra">PMID:19233199</ref><references group="xtra"/>
-[[Category: Aldehyde reductase]]
 [[Category: Homo sapiens]]
-[[Category: Ginell, S.]]
+[[Category: Large Structures]]
-[[Category: Hazemann, I.]]
+[[Category: Ginell S]]
-[[Category: Joachimiak, A.]]
+[[Category: Hazemann I]]
-[[Category: Mitschler, A.]]
+[[Category: Joachimiak A]]
-[[Category: Petrova, T.]]
+[[Category: Mitschler A]]
-[[Category: Podjarny, A.]]
+[[Category: Petrova T]]
-[[Category: Acetylation]]
+[[Category: Podjarny A]]
-[[Category: Cataract]]
-[[Category: Cytoplasm]]
-[[Category: Nadp]]
-[[Category: Oxidoreductase]]
-[[Category: Phosphoprotein]]
-[[Category: Polymorphism]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  1 09:13:50 2009''