It sounds like your id_numbers.txt file has DOS/Windows-style line endings (carriage return followed by linefeed characters) instead of plain unix line endings (just linefeed). The result is that read thinks the line ends with a carriage return, $line actually has a carriage return at the end, and that gets embedded in the url, causing various confusion.
There are several ways to solve this. You could have bash trim the carriage return from the variable when you use it:
url="http://www.rcsb.org/pdb/files/${line%$'\r'}.pdb"
Or you could have read trim it by telling it that carriage return counts as whitespace (read will trim leading and trailing whitespace from what it reads):
while IFS=$'\r' read line
Or you could use a command like dos2unix (or whatever the equivalent is on your OS) to convert the id_numbers.txt file.
