1KFA

Crystal structure of Fab fragment complexed with gibberellin A4

Summary for 1KFA

• Entry DOI: 10.2210/pdb1kfa/pdb
• Descriptor: monoclonal antibody light chain, monoclonal antibody heavy chain, GIBBERELLIN A4, ... (4 entities in total)
• Functional Keywords: immunoglobuiln fold, immune system
• Biological source: Mus musculus (mouse); More
• Total number of polymer chains: 4
• Total formula weight: 95695.13

Authors

Murata, T.,Fushinobu, S.,Nakajima, M.,Asami, O.,Sassa, T.,Wakagi, T.,Yamaguchi, I. (deposition date: 2001-11-20, release date: 2002-09-11, Last modification date: 2024-10-23)

Primary citation

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., 293:489-496, 2002

PubMed Abstract: 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.

PubMed: 12054627
DOI: 10.1016/S0006-291X(02)00225-5

Experimental method

X-RAY DIFFRACTION (2.8 Å)