US city in south, one that is protected by alien god (3,5)
I believe the answer is:
san diego
'us city' is the definition.
(San Diego is a city in California)
'south one that is protected by alien god' is the wordplay.
'south' becomes 's' (abbreviation).
'one' becomes 'an' (an apple is one apple).
'that is' becomes 'ie' (short for Latin 'id est', 'that is').
'protected by' is an insertion indicator.
'alien' indicates anagramming the letters.
'god' anagrammed gives 'dgo'.
'ie' placed inside 'dgo' is 'diego'.
's'+'an'+'diego'='SAN DIEGO'
'in' acts as a link.
(Other definitions for san diego that I've seen before include "Calif. naval base" , "Californian resort" , "Californian port" , "Agonised over the Californian city" , "City of S. California" .)