No reason to get excited. Here is how I would usually do it by iterating directly over the structure.

my $position = 1200;
for my $s (@$data) {
    next unless $s->{PROT_NAME} eq 'ALK';
    foreach my $p ( @{ $s->{PDBS} } ) {
        foreach my $b ( @{ $p->{BLOCKS} } ) {
            if ($position >= $b->{PSTART} && $position <= $b->{PEND} )
+{
                print ($p->{PDB_ID},"\n");
            }
        }
    }
}
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