5YD3

Crystal structure of the scFv antibody 4B08 with epitope peptide

Summary for 5YD3

• Entry DOI: 10.2210/pdb5yd3/pdb
• Descriptor: scFv 4B08, Epitope peptide, SULFATE ION, ... (5 entities in total)
• Functional Keywords: antibody, biomolecular recognition, md simulations, thermodynamics, immune system
• Biological source: Mus musculus; More
• Total number of polymer chains: 8
• Total formula weight: 112451.66

Authors

Caaveiro, J.M.M.,Miyanabe, K.,Tsumoto, K. (deposition date: 2017-09-11, release date: 2018-06-06, Last modification date: 2024-10-23)

Primary citation

Miyanabe, K.,Akiba, H.,Kuroda, D.,Nakakido, M.,Kusano-Arai, O.,Iwanari, H.,Hamakubo, T.,Caaveiro, J.M.M.,Tsumoto, K.
Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody
J. Biochem., 164:65-76, 2018

PubMed Abstract: Molecular recognition is a fundamental event at the core of essentially every biological process. In particular, intermolecular H-bonds have been recognized as key stabilizing forces in antibody-antigen interactions resulting in exquisite specificity and high affinity. Although equally abundant, the role of intramolecular H-bonds is far less clear and not universally acknowledged. Herein, we have carried out a molecular-level study to dissect the contribution of intramolecular H-bonds in a flexible peptide for the recognition by an antibody. We show that intramolecular H-bonds may have a profound, multifaceted and favorable effect on the binding affinity by up to 2 kcal mol-1 of free energy. Collectively, our results suggest that antibodies are fine tuned to recognize transiently stabilized structures of flexible peptides in solution, for which intramolecular H-bonds play a key role.

PubMed: 29924367
DOI: 10.1093/jb/mvy032

Experimental method

X-RAY DIFFRACTION (1.35 Å)