What about where we don't have control over the issuing of reqs to CAs, as in a large company where cert reqs all go through a specific dept?

I have had certs issued for me, so I have the .pfx and .cer files, but when I try to use them in a keystore (using keytool), I get an exception: javax.net.ssl.SSLHandshakeException: no cipher suites in common.

Is it possible to convert a .cer file into a Java keystore or do I need to have generated the request using the same alias etc.?