Capital is of a different organisation (5)
I believe the answer is:
sofia
'capital' is the definition.
(capital of Bulgaria)
'is of a different organisation' is the wordplay.
'a different' is an anagram indicator (letters placed in a different order).
'organisation' becomes 'a' (I can't justify this - if you can you should believe this answer much more).
'is'+'of'='isof'
'isof' is an anagram of 'sofi'.
'sofi'+'a'='SOFIA'
Can you help me to learn more?
(Other definitions for sofia that I've seen before include "capital city" , "seat of government" , "European city" , "Balkan capital" , "Foreign city" .)