I'm not sure what format .pub is, but from the Putty "Help" documentation there appear to be several open formats available for the public key. Fire up puttygen and check out the Conversions tab--neither says ".pub format", but my guess is the OpenSSH or ssh.com format is the one--you will just have to try them both and see what works.
You can also go the other route and have the key generated on the remote system and try importing the private key into your Putty key chain. That might work too and will guarantee its compatible with the remote system.
Once you get that working, get Filezilla and load your key into that--then the world is your oyster! You can connect to any ssh and sftp files with a pretty gui.
Good Luck.