PCI-E and AGP are different types of slot connector on graphics cards. AGP cards cannot work in PCI-E motherboards, and PCI-E cards cannot work in AGP slots. The only real difference between the two is that PCI-E is newer and can usually support SLi or Crossfire (two graphics cards at once).
Here are what the slot connectors look like: -
This is an AGP slot connector.
This is a PCI-E slot connector.
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