Beyond these major bodies, there are a host of other smaller institutions which run various aspects of the EU. These range from the Committee of the Regions which gives local government (which included Scottish councils) a voice in Brussels, to the European Investment Bank which lends to capital infrastructure projects (such as hospitals in Scotland).
For the common market to function, many of these structures are not only desirable, but necessary. In fact, if you were to design a system to regulate a common market from scratch it would probably look remarkably similar to the EU!
There are of course a host of smaller bodies, more details of which can be found by clicking here.