#!/usr/bin/perl
use warnings;
use strict;

my $line = "BOGUS PPI3_SYNY3 276 aa linear BCT 13-NOV-2019\n";

if (my ($bogus, $acids) = $line =~ /BOGUS\s+([A-Z0-9_]+) ([0-9]+ [a-z]
++)/) {
    print "bogus: $bogus\nNumber of acids: $acids\n"
}
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Your code is unfortunately incomplete. How did you populate $noOfAcids? Also, $ in the second regex can't match after "aa", as the string doesn't end there. Note that $1 et al. are only changed after a successful match, so if the second regex doesn't match, the value of $1 keeps the value from the previous match.