Nodding, agent accepts shelter (6)
I believe the answer is:
sleepy
'nodding' is the definition.
(I've seen this before)
'agent accepts shelter' is the wordplay.
'agent' becomes 'spy' (spy is a kind of agent).
'accepts' means one lot of letters goes inside another.
'shelter' becomes 'lee' (as in lee side, the side sheltered from wind).
'spy' enclosing 'lee' is 'SLEEPY'.
(Other definitions for sleepy that I've seen before include "in retirement?" , "Doc's nodding pal" , "over-tired" , "(Of place) without much activity" , "Feeling like having a snooze" .)