3grs: Difference between revisions

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-{{Seed}}
-[[Image:3grs.png|left|200px]]
-<!--
+==REFINED STRUCTURE OF GLUTATHIONE REDUCTASE AT 1.54 ANGSTROMS RESOLUTION==
-The line below this paragraph, containing "STRUCTURE_3grs", creates the "Structure Box" on the page.
+<StructureSection load='3grs' size='340' side='right'caption='[[3grs]], [[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'>[[3grs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2grs 2grs] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1grs 1grs]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GRS 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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_3grs|  PDB=3grs  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3grs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3grs OCA], [https://pdbe.org/3grs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3grs RCSB], [https://www.ebi.ac.uk/pdbsum/3grs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3grs ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GSHR_HUMAN GSHR_HUMAN] Maintains high levels of reduced glutathione in the cytosol.
+== 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/gr/3grs_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=3grs ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of human glutathione reductase has been established at 1.54 A resolution using a restrained least-squares refinement method. Based on 77,690 independent reflections of better than 10 A resolution, a final R-factor of 18.6% was obtained with a model obeying standard geometry within 0.025 A in bond lengths and 2.4 degrees in bond angles. The final 2Fo-Fc electron density map allows for the distinction of carbon, nitrogen and oxygen atoms with temperature factors below about 25 A2. Apart from 461 amino acid residues and the prosthetic group FAD, the model contains 524 solvent molecules, about 118 of which can be considered an integral part of the enzyme. The largest solvent cluster is at the dimer interface and contains 104 interconnected solvent molecules, part of which are organized in a warped sheet-like structure. The main-chain dihedral angles are well-concentrated in the allowed regions of the Ramachandran plot. The spread of dihedral angles in beta-pleated sheets is much larger than in alpha-helices and especially in alpha-helix cores, indicating the higher plasticity of beta-structures. The analysis revealed a large amount of 3(10)-helix. The side-chain conformations cluster at the staggered positions, and show well-defined preferences. Also, a mobility gradient is observed for side-chains. Non-polar and polar side-chains show average temperature factor increases per bond of 10% and 25%, respectively. A number of alternative conformations of internal side-chains, in particular serines and methionines, have been detected. The extended FAD molecule also shows a mobility gradient between the very rigid flavin (mean value of B) = 8.7 A2) and the more mobile adenine (mean value of B = 16.2 A2). The entire active center is particularly well ordered, with temperature factors around 10 A2. The dimer interface consists of a rigid contact area, which is well conserved in the Escherichia coli enzyme, and a flexible area that is not. Altogether, the buried surfaces at the crystal contacts are half as large as at the dimer interface, but less specific. The refined structure shows clearly that there are no buried cations compensating the charge of the pyrophosphate moiety of FAD. The flavin deviates slightly from standard geometry, which is possibly caused by the polypeptide environment. In contrast to an earlier interpretation, atom N5 of the flavin can accommodate a proton, and it is conceivable that this proton proceeds to the redox-active disulfide.(ABSTRACT TRUNCATED AT 400 WORDS)
-===REFINED STRUCTURE OF GLUTATHIONE REDUCTASE AT 1.54 ANGSTROMS RESOLUTION===
+Refined structure of glutathione reductase at 1.54 A resolution.,Karplus PA, Schulz GE J Mol Biol. 1987 Jun 5;195(3):701-29. PMID:3656429<ref>PMID:3656429</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3grs" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_3656429}}, adds the Publication Abstract to the page
+*[[Glutathione Reductase|Glutathione Reductase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 3656429 is the PubMed ID number.
+*[[Rossmann fold|Rossmann fold]]
--->
+== References ==
-{{ABSTRACT_PUBMED_3656429}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-GRS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entries  and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1grs 1grs]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRS OCA].
-==Reference==
-Refined structure of glutathione reductase at 1.54 A resolution., Karplus PA, Schulz GE, J Mol Biol. 1987 Jun 5;195(3):701-29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/3656429 3656429]
-[[Category: Glutathione-disulfide reductase]]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Karplus, P A.]]
+[[Category: Karplus PA]]
-[[Category: Schulz, G E.]]
+[[Category: Schulz GE]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 16:19:15 2008''