5YD3

Crystal structure of the scFv antibody 4B08 with epitope peptide

5YD3 の概要

• エントリーDOI: 10.2210/pdb5yd3/pdb
• 分子名称: scFv 4B08, Epitope peptide, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: antibody, biomolecular recognition, md simulations, thermodynamics, immune system
• 由来する生物種: Mus musculus; 詳細
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 112451.66

構造登録者

Caaveiro, J.M.M.,Miyanabe, K.,Tsumoto, K. (登録日: 2017-09-11, 公開日: 2018-06-06, 最終更新日: 2024-10-23)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.35 Å)