Department containing nothing but a storehouse (5)
I believe the answer is:
depot
'a storehouse' is the definition.
(synonyms)
'department containing nothing' is the wordplay.
'department' becomes 'dept'.
'containing' means one lot of letters goes inside another.
'nothing' becomes 'O' (looks like zero - 0).
'dept' going around 'o' is 'DEPOT'.
'but' acts as a link.
(Other definitions for depot that I've seen before include "Military HQ" , "Storage location" , "Storage place" , "Bus station or warehouse" , "Toped (anag.)" .)