my %hash;  # somewhere before you start to loop over the data
...
# within the loop over your data
my $signature = join '|', $id2, $sequence;
my $structure = {
  id1 => $id1,
  id2 => $id2,
  sequence => $sequence,
  label => $label,
};
$hash{$signature} = $structure;  # save it

##</code><code>##

for my $signature (keys %hash) {
  my $structure = $hash{$signature};
  printf "%s|%s\n%s\n%s\n",
      $structure->{id1},
      $structure->{id2},
      $structure->{sequence},
      $structure->{label};
}