When you see Using Index in the Extra part of an explain it means that the (covering) index is adequate for the query.
In your example: SELECT id FROM test WHERE id = 5; the server doesn’t need to access the actual table as it can satisfy the query (you only access id) only using the index (as the explain says). In case you are not aware the PK is implemented via a unique index.
When you see Using Index; Using where it means that first the index is used to retrieve the records (an actual access to the table is not needed) and then on top of this result set the filtering of the where clause is done.
In this example: SELECT id FROM test WHERE id > 5; you still fetch for id from the index and then apply the greater than condition to filter out the records non matching the condition