。
The train is scheduled to leave in five minutes.
Literal
Train [topic-は] after 5-minutes [in-で] departs [should-はず] [copula-です].
あと ('after, remaining') paired with a duration means 'X from now.' で here marks the timeframe ('in, within') — distinct from the spatial/instrumental で. ~はずです marks scheduled expectation. Notice how Japanese piles up pre-verbal modifiers before 出発する: all the temporal framing is set up before the verb arrives at the end.