1q4e: Difference between revisions

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-{{Seed}}
-[[Image:1q4e.png|left|200px]]
-<!--
+==S65T Q80R Y145C Green Fluorescent Protein (GFP) pH 8.5==
-The line below this paragraph, containing "STRUCTURE_1q4e", creates the "Structure Box" on the page.
+<StructureSection load='1q4e' size='340' side='right'caption='[[1q4e]], [[Resolution|resolution]] 1.38&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'>[[1q4e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q4E 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]] 1.38&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>
-{{STRUCTURE_1q4e|  PDB=1q4e  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q4e OCA], [https://pdbe.org/1q4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q4e RCSB], [https://www.ebi.ac.uk/pdbsum/1q4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q4e ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
+== 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/q4/1q4e_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=1q4e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Atomic resolution structures of proteins indicate that the core is typically well packed, suggesting a densely connected network of interactions between amino acid residues. The combinatorial complexity of energetic interactions in such a network could be enormous, a problem that limits our ability to relate structure and function. Here, we report a case study of the complexity of amino acid interactions in a localized region within the core of the GFP, a particularly stable and tightly packed molecule. Mutations at three sites within the chromophore-binding pocket display an overlapping pattern of conformational change and are thermodynamically coupled, seemingly consistent with the dense network model. However, crystallographic and energetic analyses of coupling between mutations paint a different picture; pairs of mutations couple through independent "hotspots" in the region of structural overlap. The data indicate that, even in highly stable proteins, the core contains sufficient plasticity in packing to uncouple high-order energetic interactions of residues, a property that is likely general in proteins.
-===S65T Q80R Y145C Green Fluorescent Protein (GFP) pH 8.5===
+Local complexity of amino acid interactions in a protein core.,Jain RK, Ranganathan R Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):111-6. Epub 2003 Dec 18. PMID:14684834<ref>PMID:14684834</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1q4e" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14684834}}, adds the Publication Abstract to the page
+*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14684834 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14684834}}
+__TOC__
+</StructureSection>
-==About this Structure==
-Q4E is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q4E OCA].
-==Reference==
-Local complexity of amino acid interactions in a protein core., Jain RK, Ranganathan R, Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):111-6. Epub 2003 Dec 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14684834 14684834]
 [[Category: Aequorea victoria]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Jain, R K.]]
+[[Category: Jain RK]]
-[[Category: Ranganathan, R.]]
+[[Category: Ranganathan R]]
-[[Category: Chromophore]]
-[[Category: Fluorophore]]
-[[Category: Gfp]]
-[[Category: Green fluorescent protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 12:50:59 2008''