I have CURATE and the answer is 6 letters not five
No 2 is something to do with EGG re 2d see clue (Curate's Egg)
Crate = quantity of bottles
second in pub = U ie pUb
yes, the answer is curate, but the reference to no.2 also applies to no.2 in a pub - i.e. who is second in command, as it were. That definition is in Chambers.
My parsing maybe wrong as far as curate is concerned, I don't have a Chambers and haven't solved 2d yet! I just noticed the first word of the clue was eggs and associated curate's egg! and parsed the rest of the clue
the answer has nothing to do with 2D. The relevant definition of curate can be found in Chambers. This is one of those clues where the entire clue is the definition, as well as showing the construction of the answer.