This study investigates the regulatory mechanisms of protein arginine deiminase 4 (PAD4) using unbiased antibody selections to identify functional antibodies that can either activate or inhibit PAD4 activity. Through cryogenic-electron microscopy (cryo-EM), the structures of these antibodies in complex with PAD4 were characterized, revealing insights into their mechanisms of action. The antibodies modulate PAD4 activity by interacting with allosteric binding sites adjacent to the catalytic pocket, leading to alterations in the active site conformation or the enzyme's oligomeric state. The study highlights the potential of using PAD4 agonist and antagonist antibodies for studying PAD4-dependent processes in disease models and future therapeutic development. The findings provide new mechanisms for enzyme regulation and suggest that PAD4 can be targeted for therapeutic intervention in autoimmune diseases such as rheumatoid arthritis (RA).This study investigates the regulatory mechanisms of protein arginine deiminase 4 (PAD4) using unbiased antibody selections to identify functional antibodies that can either activate or inhibit PAD4 activity. Through cryogenic-electron microscopy (cryo-EM), the structures of these antibodies in complex with PAD4 were characterized, revealing insights into their mechanisms of action. The antibodies modulate PAD4 activity by interacting with allosteric binding sites adjacent to the catalytic pocket, leading to alterations in the active site conformation or the enzyme's oligomeric state. The study highlights the potential of using PAD4 agonist and antagonist antibodies for studying PAD4-dependent processes in disease models and future therapeutic development. The findings provide new mechanisms for enzyme regulation and suggest that PAD4 can be targeted for therapeutic intervention in autoimmune diseases such as rheumatoid arthritis (RA).