2bjm
From Proteopedia
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SPE7:ANTHRONE COMPLEX
Overview
Induced fit is a predominant phenomenon in protein-ligand interactions, yet it is invariably attributed without establishing the existence, let, alone the structure, of the initial, low-affinity encounter complex. We, determined the crystal structure of the encounter complex on the pathway, of ligand binding by IgE antibody SPE7. We show that this complex is, formed by a wide range of ligands that initially bind with identical, affinity. Nonspecific ligands rapidly dissociate, whereupon the antibody, isomerizes to a nonbinding isomer. Specific ligand complexes, however, slowly isomerize to give a high-affinity complex. This isomerization, involves backbone and side-chain rearrangements of up to 14 A and the, formation of specific hydrogen bonds. The postbinding conformational, switch, combined with the prebinding isomerization to an energetically, favorable nonbinding isomer, results in a "kinetic discrimination", mechanism that mediates selective binding, by a factor of >10(3), between, highly related ligands that initially bind with the same affinity. This, model may apply to proteins that bind multiple ligands in a specific, manner or other proteins that, although capable of binding many ligands, are activated by only a few.
About this Structure
2BJM is a Single protein structure of sequence from Rattus rattus with ANF as ligand. Known structural/functional Site: . Full crystallographic information is available from OCA.
Reference
Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition., James LC, Tawfik DS, Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12730-5. Epub 2005 Aug 29. PMID:16129832
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