This is the syntax of creating primary key
db.< collection >.createIndex( < key and index type specification>, { unique: true } )
Let's take that our database have collection named student and it's document have key named student_id which we need to make a primary key. Then the command should be like below.
db.student.createIndex({student_id:1},{unique:true})
You can check whether this student_id set as primary key by trying to add duplicate value to the student collection.
prefer this document for further informations https://docs.mongodb.com/manual/core/index-unique/#create-a-unique-index