Lima, an extraordinary capital city (6)
I believe the answer is:
manila
'capital city' is the definition.
'lima an extraordinary' is the wordplay.
'extraordinary' indicates an anagram.
'lima'+'an'='limaan'
'limaan' is an anagram of 'MANILA'.
(Other definitions for manila that I've seen before include "Adulterated, tainted" , "Strong brown paper originally made from hemp" , "Brown paper and Philippine city" , "Animal found in Philippines" , "Animal or capital in the Phillipines" .)