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1kfa

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Crystal structure of Fab fragment complexed with gibberellin A4

Structural highlights

1kfa is a 4 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Murata T, Fushinobu S, Nakajima M, Asami O, Sassa T, Wakagi T, Yamaguchi I. Crystal structure of the liganded anti-gibberellin A(4) antibody 4-B8(8)/E9 Fab fragment. Biochem Biophys Res Commun. 2002 Apr 26;293(1):489-96. PMID:12054627 doi:10.1016/S0006-291X(02)00225-5

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1kfa"

@@ Line 3: / Line 3: @@
 <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/Lk3_transgenic_mice Lk3 transgenic mice]. 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>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GA4:GIBBERELLIN+A4'>GA4</scene></td></tr>
+</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></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>
@@ Line 35: / Line 35: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Lk3 transgenic mice]]
+[[Category: Mus musculus]]
-[[Category: Asami, O]]
+[[Category: Asami O]]
-[[Category: Fushinobu, S]]
+[[Category: Fushinobu S]]
-[[Category: Murata, T]]
+[[Category: Murata T]]
-[[Category: Nakajima, M]]
+[[Category: Nakajima M]]
-[[Category: Sassa, T]]
+[[Category: Sassa T]]
-[[Category: Wakagi, T]]
+[[Category: Wakagi T]]
-[[Category: Yamaguchi, I]]
+[[Category: Yamaguchi I]]
-[[Category: Immune system]]
-[[Category: Immunoglobuiln fold]]

1kfa

From Proteopedia

Current revision

Crystal structure of Fab fragment complexed with gibberellin A4

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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