The City 17 Citadel is the most important Citadel for the Combine, this is the base of their operations.
The Citadel was the headquarters from which the Combine govern the Earth.
Its associated portal is the primary means of communication with offworld Combine forces. The super portal is probably how the Citadel came to Earth.
It was located in City 17, and resembled a massive skyscraper, rising several kilometers into the sky from ground level, and extending some distance underground as well.
Before reaching the very top of the citadel, Freeman passes through many open areas of the citadel where enormous segments of the citadel exterior wall open and close to allow Dropships and gunships to quickly exit and enter the citadel's interior.
In the first few chapters of Half-Life 2: Episode One, the player is given a firsthand look at much of the lower levels of the Citadel.
Whilst mostly looking very much the same as the rest of the Citadel, no war factories or synth manufacturing plants are located in this area of the structure.