The introduction of the Accelerated Graphics Port (AGP) did not make the conventional PCI bus on motherboards obsolete in the same way that PCI gradually squeezed out ISA slots.
AGP-based motherboards have some slight architectural changes that make them stand out from motherboards that only have PCI slots. Motherboard chipsets have to be created in a manner that they will accept new instruction types from AGP devices.
Both AGP- and PCI-based motherboards usually have at least one PCI slot. AGP was not created to replace PCI, but to create a new dedicated bus that would provide all its resources to the function of the graphics cards.
Any graphics card plugged into an AGP slot will have total control of the resources that have been given to that bus. PCI cards normally have to share the bus with other cards, because motherboards usually have more than one PCI slot.
The AGP slot in a motherboard stands out because of its displaced location and the fact that it usually sits just above the PCI bus.
The innovation of AGP led to the creation of PCI Express, which superseded PCI and intends to completely replace it. PCI Express has a serial connection, meaning that each device on the bus can have equal attention, and all of them are practically dedicated.