Usually the graphics card requirement is only important in a few operations 3D and has no bearing on installation or general use of the program. Now, if you want to animate, you're talking about a whole different animal. But system requirements are also the minimum. It wants at least an AGP card and you have a PCI Express X 16 which, as you say, is more advanced, so you're good to go.
As for PCI vs. AGP, one advantage that AGP always had over PCI and still has over PCI Express ports is that, if you use all the built-in RAM from your AGP card, it can draw extra RAM from your system RAM, giving it a maximum that's much higher than what comes on the card. Even PCI Express X 16 can't do that.