The most common and most likely answer to this crossword clue is the 5 letter word APSIS
I've seen this crossword clue in The Times
A
P
S
I
S
More clues leading to the result APSIS
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The straight part
We know that "part of church" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case part of church = apsis.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does APSIS mean?
APSIS noun- A recess or projection, with a dome or vault, at the east end of a church; an apse.
- Either of the points in the elliptical orbit of a planet or comet where it is closest or furthest from the sun; perihelion or aphelion; an apside