@sudhirpratapyadav i am just another user, and cannot reproduce this in 5.0. can you confirm if the box have physics API applied? (rigid body and/or collider). and to test whether it’s related to an extension, could you try loading one of the physics examples (Window > Examples > Physics Examples > Basics > Box on a table), are you able to use the Shift + LMB once the box has landed onto the table?
also, did you set up the USD in 4.5 and then opening it up in 5.0? or did you create both scenes from scratch in each version?