Is this operating contract valid?

In March 2008, A, B and C, who are all US citizens based in San Francisco, enter into an Operating Agreement for their newly formed California Limited Liability Company. Each of the parties has signed the agreement by logging into a website with their personal username and password and clicking on an ‘Agree’ button after having the chance to scroll through and read the agreement.

Answer

I would ask an attorney about this one. There might be an electronic signature act that covers these types of agreements.

Is there no paper document as well?

Courts are very old fashioned, and they like paper (if this were to ever go to court).