Kondukter je rekao da naš kupe nije u prvom, nego u zadnjem vagonu.

Je rekao is the standard Croatian past tense (often called the perfect).

It is formed with:

• the present-tense auxiliary je = is/has (from biti, to be)
• the past participle rekao = said

So:

• Kondukter je rekao = The conductor said

Because kondukter is masculine singular, the participle is rekao. Compare:

• Kondukterica je rekla = The female conductor said

Because je is a clitic. In Croatian, clitics usually go in the second position in the clause.

So:

• Kondukter je rekao... is natural
• not normally Je kondukter rekao... in a neutral statement

This second-position rule is very common in Croatian and affects forms like:

• je, sam, si, smo, ste, su
• short pronouns like ga, mu, se, etc.

Da introduces a subordinate clause, here meaning that.

So:

• rekao da... = said that...

English often drops that:

• The conductor said our compartment...

But Croatian normally keeps da:

• Kondukter je rekao da naš kupe...

After verbs like reći (to say), misliti (to think), znati (to know), vidjeti (to see), this is very common.

Because kupe is treated as a masculine singular noun in Croatian.

So the possessive adjective must agree with it:

• naš kupe = our compartment

Even though kupe ends in -e, it is not neuter here. It is one of those borrowed nouns that do not behave like a typical native noun ending.

Agreement tells you the gender:

• masculine: naš
• feminine: naša
• neuter: naše

Since the sentence has naš, that tells you kupe is masculine.

Usually no: kupe is commonly treated as an indeclinable noun, meaning its form stays the same.

So you may see:

• naš kupe
• u kupeu is sometimes encountered in practice, but for learners, it is safest to think of kupe as mostly not changing in standard everyday use

What does clearly show the grammar around it is the adjective:

• naš kupe
• našem kupeu / našem kupeu may appear in some usage patterns, but this is exactly why learners often find the word messy

For practical learning, the important point in this sentence is:

• kupe is masculine
• naš agrees with it

Because the negative form of je is nije.

This is just the standard form:

• je = is
• nije = is not

So:

• naš kupe nije... = our compartment is not...

Croatian does this with forms of biti:

• sam → nisam
• si → nisi
• je → nije
• smo → nismo
• ste → niste
• su → nisu

Here u means in, so it expresses location, not movement. With location, u takes the locative case.

That is why you get:

• u prvom (vagonu)
• u zadnjem vagonu

Both prvom and zadnjem are locative singular masculine forms, matching vagonu.

Compare:

• location: u prvom vagonu = in the first carriage
• movement: u prvi vagon = into the first carriage

So:

• u + locative = being in
• u + accusative = going into

Because Croatian often omits a repeated noun when it is obvious from context.

So:

• u prvom, nego u zadnjem vagonu

really means:

• u prvom vagonu, nego u zadnjem vagonu

This is very natural and avoids repetition. English does the same thing sometimes:

• not in the first, but in the last carriage

Here prvom works like the first one.

Because Croatian normally uses nego after a negation when the second part replaces/corrects the first.

Pattern:

• ne..., nego... = not..., but rather...

So:

• nije u prvom, nego u zadnjem vagonu = it isn’t in the first, but in the last carriage

Ali means but, but it is not the best choice in this correction pattern.

Compare:

• Ne kavu, nego čaj. = Not coffee, but tea.
• Nije prvi, nego zadnji. = It’s not the first, but the last.

So this sentence uses a very common Croatian structure:

• ne / nije ... nego ...

In this sentence, zadnjem vagonu most naturally means the last carriage, and in train context that also often implies the rear carriage.

The adjective zadnji can mean:

• last in a sequence
• rear/back depending on context

You may also learn:

• posljednji = last (often a bit more explicitly “last in sequence”)

In everyday Croatian, zadnji vagon is completely natural for the last carriage.

Yes. That would also be correct.

Full version:

• Kondukter je rekao da naš kupe nije u prvom vagonu, nego u zadnjem vagonu.

Shorter version in your sentence:

• Kondukter je rekao da naš kupe nije u prvom, nego u zadnjem vagonu.

The shorter version sounds natural because Croatian often avoids repeating a noun that is already clear.

Croatian word order is fairly flexible, but this sentence has a very natural neutral order.

Standard version:

• Kondukter je rekao da naš kupe nije u prvom, nego u zadnjem vagonu.

You can move parts around for emphasis, but not all versions sound equally natural. For example:

• Kondukter je rekao da naš kupe nije u zadnjem vagonu, nego u prvom.
  This would change the meaning/emphasis.
• Naš kupe nije u prvom, nego u zadnjem vagonu, rekao je kondukter.
  Also possible, but more literary or marked.

For learners, the given order is the best one to imitate.