3kdm: Difference between revisions

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-[[Image:3kdm.png|left|200px]]
-<!--
+==Crystal Structure of Human Anti-steroid Fab 5F2 in Complex with Testosterone==
-The line below this paragraph, containing "STRUCTURE_3kdm", creates the "Structure Box" on the page.
+<StructureSection load='3kdm' size='340' side='right'caption='[[3kdm]], [[Resolution|resolution]] 1.50&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'>[[3kdm]] is a 4 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=3KDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KDM 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]] 1.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=TES:TESTOSTERONE'>TES</scene></td></tr>
-{{STRUCTURE_3kdm|  PDB=3kdm  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kdm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kdm OCA], [https://pdbe.org/3kdm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kdm RCSB], [https://www.ebi.ac.uk/pdbsum/3kdm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kdm 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/kd/3kdm_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=3kdm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A testosterone binding scFv antibody was isolated from a naive human library with a modest size of 10(8) clones. The crystal structure of the Fab fragment form of the 5F2 antibody clone complexed with testosterone determined at 1.5 A resolution shows that the hapten is bound deeply in the antibody binding pocket. In addition to the interactions with framework residues only CDR-L3 and CDR-H3 loops interact with testosterone and the heavy chain forms the majority of the contacts with the hapten. The testosterone binding site of the 5F2 antibody with a high abundance of aromatic amino acid residues shows similarity with an in vitro affinity matured antibody having around 300 times higher affinity. The moderate affinity of the 5F2 antibody originates from the different orientation of the hapten and few light chain contacts. This is the first three-dimensional structure of a human steroid hormone binding antibody that has been isolated from a naive human repertoire.
-===Crystal Structure of Human Anti-steroid Fab 5F2 in Complex with Testosterone===
+The testosterone binding mechanism of an antibody derived from a naive human scFv library.,Niemi MH, Takkinen K, Amundsen LK, Soderlund H, Rouvinen J, Hoyhtya M J Mol Recognit. 2011 Mar-Apr;24(2):209-19. doi: 10.1002/jmr.1039. PMID:21360611<ref>PMID:21360611</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3kdm" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[3kdm]] is a 4 chain structure with 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=3KDM OCA].
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[3D structures of human antibody|3D structures of human antibody]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Niemi, M H.]]
+[[Category: Large Structures]]
-[[Category: Rouvinen, J.]]
+[[Category: Niemi MH]]
+[[Category: Rouvinen J]]