Hey, i am not pretty sure about that, but i think that in order to get that 5V through the aforementioned pin you have to get power from an external power supply (and specifically via the 5V DC barrel connector input) and not (only) from the usb cable.
Also, you have to keep in mind that the usage of the external 5VDC supply is necessary if the external circuit that you are going to use (if you are going to use any) or let's say a cape that you use, is "power hungry".
Hope that solves your problem and you don't have a damaged board!