We are evaluating the use of Microsoft Secure Productive Enterprise. Which use rights are granted by a Secure Productive Enterprise license and which are the differences between E3 and E5?
Secure Productive Enterprise is a user subscription combining Office 365 (E3 or E5), Enterprise Mobility + Security (EMS) (E3 or E5), and Windows 10 Enterprise (E3 or E5) in one suite product.
Moreover, Secure Productive Enterprise grants the use rights to SharePoint, Exchange, and Skype for Business Server for in-house operations.
Additionally, Office 365 (E3 or E5) contains dual access rights which grants access to the associated servers in ones own data center. The same applies to Enterprise Mobility + Security which provides the access licenses which are not included in Office 365 (E3 or E5). Hence, Secure Productive Enterprise contains all server access licenses (CALs), which otherwise must be purchased separately.
In comparison to Secure Productive Enterprise E3, the E5 license grants the use of Microsoft Power BI Pro and Microsoft MyAnalytics.

Sources:
Licensing Secure Productive Enterprise_as is 2017-03-29
Microsoft Secure Productive Enterprise components_as is 2017-11-09