It sounds like you already have a /home/user/.q3a/baseq3/ directory, to verify that this is the case, type in the following:

It shouldn't return an error but it should display the files in there, I think there's a .cfg file in there or something by default, but as long as it doesn't say "No such file or directory" you're good.

Now, assuming you moved your pk3 files into the baseq3 folder inside of MyDocs as qole suggested, now run this to move them into your quake 3 arena folder where they should go:

(edit: made a mistake :'( )

And that will move all the files from the directory inside MyDocs into your quake 3 arena folder. To verify they're there, you can again run:

and you should see some pk3 files, this is what mine looks like: "crashlog.txt pak0.pk3 pak1.pk3 q3config.cfg q3history"

You should now be able to run quake3 and it should start up pretty quickly asking you for a key, and you just hit enter there. Let us know exactly what happens when you try to run it if it still isn't working.

Sorry if that was too verbose, not sure what your linux experience is