6A79

Crystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with the mutant scFv fragment (P103A) of murine monoclonal antibody B5209B

Summary for 6A79

• Entry DOI: 10.2210/pdb6a79/pdb
• Descriptor: Roundabout homolog 1, Light chain region of the anti-human Robo1 antibody B5209B scFv, Heavy chain of the anti-human Robo1 antibody B5209B scFv, ... (5 entities in total)
• Functional Keywords: hepatocellular carcinoma antigen, angiogenesis, immune system, antibody drug, single-chain variable fragment
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 6
• Total formula weight: 72440.59

Authors

Mizohata, E.,Nakayama, T.,Kado, Y.,Yokota, Y.,Inoue, T. (deposition date: 2018-07-02, release date: 2019-01-30, Last modification date: 2024-10-30)

Primary citation

Yamashita, T.,Mizohata, E.,Nagatoishi, S.,Watanabe, T.,Nakakido, M.,Iwanari, H.,Mochizuki, Y.,Nakayama, T.,Kado, Y.,Yokota, Y.,Matsumura, H.,Kawamura, T.,Kodama, T.,Hamakubo, T.,Inoue, T.,Fujitani, H.,Tsumoto, K.
Affinity Improvement of a Cancer-Targeted Antibody through Alanine-Induced Adjustment of Antigen-Antibody Interface.
Structure, 27:519-, 2019

PubMed Abstract: To investigate favorable single amino acid substitutions that improve antigen-antibody interactions, alanine (Ala) mutagenesis scanning of the interfacial residues of a cancer-targeted antibody, B5209B, was performed based on X-ray crystallography analysis. Two substitutions were shown to significantly enhance the binding affinity for the antigen, by up to 30-fold. One substitution improved the affinity by a gain of binding enthalpy, whereas the other substitution improved the affinity by a gain of binding entropy. Molecular dynamics simulations showed that the enthalpic improvement could be attributed to the stabilization of distant salt bridges located at the periphery of the antigen-antibody interface. The entropic improvement was due to the release of water molecules that were stably trapped in the antigen-antibody interface of the wild-type antibody. Importantly, these effects of the Ala substitutions were caused by subtle adjustments of the binding interface. These results will be helpful to design high-affinity antibodies with avoiding entropy-enthalpy compensation.

PubMed: 30595454
DOI: 10.1016/j.str.2018.11.002

Experimental method

X-RAY DIFFRACTION (2.31 Å)