I get no matches (the ID exists though).

Others have addressed the basic problem, but the statement quoted from the OP suggests something else is going on that may merit another look at the actual code (Update: and/or data).

The example below shows that a match should have occurred even without metaquoting if the string being matched against contained the 'id' string as a substring; however, the actual matched sequence would not be as expected due to regex alternation operators embedded in the 'id' string.

c:\@Work\Perl>perl -wMstrict -le
"my $id  =    '1QJ8:A|PDBID|CHAIN';
 my $str = 'xxx1QJ8:A|PDBID|CHAINxxx';
 ;;
 print qq{matched '$&'} if $str =~ /$id/;
"
matched '1QJ8:A'
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BTW: All the usual cautions against the use of  $& in production code apply — and a cooty-shot too!