1kfa: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,329,557 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,329,557 edits
No edit summary
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{STRUCTURE_1kfa|  PDB=1kfa  |  SCENE=  }}
===Crystal structure of Fab fragment complexed with gibberellin A4===
{{ABSTRACT_PUBMED_12054627}}


==About this Structure==
==Crystal structure of Fab fragment complexed with gibberellin A4==
[[1kfa]] 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=1KFA OCA].  
<StructureSection load='1kfa' size='340' side='right'caption='[[1kfa]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kfa]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KFA FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GA4:GIBBERELLIN+A4'>GA4</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kfa OCA], [https://pdbe.org/1kfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kfa RCSB], [https://www.ebi.ac.uk/pdbsum/1kfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kfa 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/kf/1kfa_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=1kfa ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Gibberellins, a class of plant hormones, consist of more than 120 members. Only a few of them are recognized by a receptor that remains unknown. The haptenic mouse monoclonal antibody, 4-B8(8)/E9, was generated against gibberellin A(4) (GA(4)) to recognize biologically active GA selectivity, and we attempted to confirm the binding properties between the antibody and GA(4). We carried out an X-ray crystallographic analysis of the 4-B8(8)/E9 Fab fragment complexed with GA(4) at a 2.8 A resolution by using the molecular replacement method. The crystal structure of the Fab fragment showed the typical immunoglobulin fold of the beta-barrel structure which is the common motif of all antibodies. A small hapten-combining site was made up of three heavy chain CDR loops. On the other hand, CDRs of the light chain did not interact directly with GA(4). The C/D rings of the GA(4) molecule were in van der Waals contact mainly with the aromatic side chain of Tyr100AH and Phe100BH of CDR-H3. The 3 beta-hydroxyl and 6 beta-carboxyl groups were, respectively, hydrogen-bonded to the main chain of Ala33H and to the Thr53H heavy chain.


==Reference==
Crystal structure of the liganded anti-gibberellin A(4) antibody 4-B8(8)/E9 Fab fragment.,Murata T, Fushinobu S, Nakajima M, Asami O, Sassa T, Wakagi T, Yamaguchi I Biochem Biophys Res Commun. 2002 Apr 26;293(1):489-96. PMID:12054627<ref>PMID:12054627</ref>
<ref group="xtra">PMID:012054627</ref><references group="xtra"/><references/>
 
[[Category: Homo sapiens]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Asami, O.]]
</div>
[[Category: Fushinobu, S.]]
<div class="pdbe-citations 1kfa" style="background-color:#fffaf0;"></div>
[[Category: Murata, T.]]
 
[[Category: Nakajima, M.]]
==See Also==
[[Category: Sassa, T.]]
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
[[Category: Wakagi, T.]]
== References ==
[[Category: Yamaguchi, I.]]
<references/>
[[Category: Immune system]]
__TOC__
[[Category: Immunoglobuiln fold]]
</StructureSection>
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Asami O]]
[[Category: Fushinobu S]]
[[Category: Murata T]]
[[Category: Nakajima M]]
[[Category: Sassa T]]
[[Category: Wakagi T]]
[[Category: Yamaguchi I]]
Retrieved from "https://proteopedia.org/1kfa"