downloadFile.do?fileFormat=FASTA&compression=NO&structureId=2CU3

##</code><code>##

>2CU3:B|PDBID|CHAIN|SEQUENCE
MVWLNGEPRPLEGKTLKEVLEEMGVELKGVAVLLNEEAFLGLEVPDRPLRDGDVVEVVALMQGG
>2CU3:A|PDBID|CHAIN|SEQUENCE
MVWLNGEPRPLEGKTLKEVLEEMGVELKGVAVLLNEEAFLGLEVPDRPLRDGDVVEVVALMQGG

##</code><code>##

   $filename =~ s[^.+/][];  # you have this one already
   $filename =~ tr/?&/_/;   # just add this one (turns all ? and & into _)