2a9n: Difference between revisions

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-{{Seed}}
-[[Image:2a9n.png|left|200px]]
-<!--
+==A Mutation Designed to Alter Crystal Packing Permits Structural Analysis of a Tight-binding Fluorescein-scFv complex==
-The line below this paragraph, containing "STRUCTURE_2a9n", creates the "Structure Box" on the page.
+<StructureSection load='2a9n' size='340' side='right'caption='[[2a9n]], [[Resolution|resolution]] 3.00&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'>[[2a9n]] is a 2 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=2A9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A9N 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]] 3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORE:4-(2,7-DIFLUORO-6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)ISOPHTHALIC+ACID'>ORE</scene></td></tr>
-{{STRUCTURE_2a9n|  PDB=2a9n  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2a9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a9n OCA], [https://pdbe.org/2a9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a9n RCSB], [https://www.ebi.ac.uk/pdbsum/2a9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a9n ProSAT]</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/a9/2a9n_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=2a9n ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of the scFv fragment FITC-E2, obtained from a naive phage antibody scFv library derived from human donors, was determined at 2.1 A resolution in the free form and at 3.0 A in the complexed form. The wild-type (wt) scFv binds fluorescein with a K(D) of 0.75 nM. The free scFv readily crystallizes by compacting its 18 amino acid-long CDR-H3, partially occluding the binding site and further blocking access by binding to the "bottom" of a neighboring scFv molecule with a cluster of exposed aromatic residues within CDR-H3. Only upon mutating one of the residues involved in this dominant crystal contact, an exposed tryptophan in the middle of CDR-H3, crystals of the complex could be obtained. A series of alanine mutants within the putative antigen binding site, covering a range of binding affinities, were used to relate macroscopic thermodynamic and kinetic binding parameters to single-molecule disruption forces measured by AFM. The effects of the mutations on the binding properties, particularly on the fraction of binding-competent molecules within the population, cannot be fully explained by changes in the strength of local interactions. The significant conformational change of CDR-H3 between the free and the liganded form illustrates the plasticity of the binding site. An accompanying study in this issue by Curcio and colleagues presents the molecular dynamics simulation of the forced unbinding experiments and explores possible effects of the mutations on the unbinding pathway of the hapten.
-===A Mutation Designed to Alter Crystal Packing Permits Structural Analysis of a Tight-binding Fluorescein-scFv complex===
+A mutation designed to alter crystal packing permits structural analysis of a tight-binding fluorescein-scFv complex.,Honegger A, Spinelli S, Cambillau C, Pluckthun A Protein Sci. 2005 Oct;14(10):2537-49. PMID:16195545<ref>PMID:16195545</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2a9n" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16195545}}, adds the Publication Abstract to the page
+*[[Antibody 3D structures|Antibody 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16195545 is the PubMed ID number.
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
--->
+*[[3D structures of human antibody|3D structures of human antibody]]
-{{ABSTRACT_PUBMED_16195545}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-A9N is a 4 chains structure of sequences 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=2A9N OCA].
+</StructureSection>
-==Reference==
-<ref group="xtra">PMID:16195545</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Cambillau, C.]]
+[[Category: Large Structures]]
-[[Category: Honegger, A.]]
+[[Category: Cambillau C]]
-[[Category: Pluckthun, A.]]
+[[Category: Honegger A]]
-[[Category: Spinelli, S.]]
+[[Category: Pluckthun A]]
-[[Category: Fluorescein]]
+[[Category: Spinelli S]]
-[[Category: Immunoglobulin]]
-[[Category: Scfv]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:49:32 2009''