Assistant covers old ship in weatherproof coat (5)
I believe the answer is:
parka
'weatherproof coat' is the definition.
'assistant covers old ship' is the wordplay.
'assistant' becomes 'PA' (personal assistant).
'covers' is an insertion indicator.
'old ship' becomes 'ark' (as in Noah's ark).
'pa' going around 'ark' is 'PARKA'.
'in' acts as a link.
(Other definitions for parka that I've seen before include "cover plus hood attachment" , "jacket for cold weather" , "weatherproof cover" , "warm gear" , "Warm, hooded coat" .)