PHP has nothing to do with the type of queries that you run on the DB.
With PHP (or any other language, platform, etc) you can do anything that the database user is allowed to do. So if you are connected to the database with a user that has administrative privileges, you can run any ALTER, CREATE, DROP statements. If you are connected with an account that only has data privileges you can run only INSERTS, UPDATES, DELETES, TRUNCATE, etc.
So the answer to your question is, yes, you can run administrative queries from a PHP script, but you need to know 2 things:
1-if the user that is connecting to the DB has administrative permissions.
2-how to write those administrative queries (they are not INSERTS).
For reference on how to write the DDL SQL commands, suggested reading:
http://dev.mysql.com/doc/refman/5.1/...efinition.html
For reference on how to manage database users:
http://dev.mysql.com/doc/refman/5.1/...anagement.html