You very much do not want to be hit by this projectile. I cannot stress this enough.
There are likely very few structures on Earth that could survive a direct hit from this Kinetic Impactor, and the ones that can are most certainly buried under many meters of solid ground.
Your best option is going to be to dodge. Electromagnetic acceleration via coil guns this powerful will give off a very distinct signature. Your ability to detect and attempt to dodge an incoming round will very much depend on your engagement distance and your ships evasive capabilities.
Given that your projectiles are moving a 1,000 km/s, any ships engaging at closer than 1,000 km had better hope they can move out of the way in less than one second.
If you cannot dodge, your second best bet is to attempt to deflect the round. Nudge its trajectory a few meters in the opposite direction from your evasive maneuvering and you might have just saved your whole ship.
Your two approaches to deflect the projectile are with your own kinetic impactor or with laser ablation. The key here is you aren't trying to stop the round, you want to apply a perpendicular acceleration to scoot it out of your way by the time it arrives.
That means pushing on one and only one side of the round. If you shoot at it from your ship, there's no way you can get enough of an angle on the incoming round to meaningfully alter its trajectory.
You also run the risk of fracturing the projectile into a cloud with mostly the same mass, moving with mostly the same velocity, but now much less predictably. Sustaining multiple hits from fragments might even be worse than a single direct hit.
If you focus a powerful enough laser on only one side of the round, you can begin pushing it in the opposite direction as bits of the projectile vaporize and push back against it. In order to meaningfully accelerate a 5000kg slug, its going to take a VERY powerful laser with VERY accurate targeting, especially if the round is rotating.
Even then I am not convinced you have enough time to meaningfully push the round out of the way.
Trying to launch an interceptor rocket for a close engagement (~1000km) is almost certainly unfeasible. Take all the problems with a kinetic interceptor and add more time required accelerate your missile.
Your rounds are slow enough, ONLY 0.3% the speed of light, that long range engagements will certainly revolve around detecting and dodging.
Even IF you had countermeasures in the form of super powerful lasers or hyper-fast missiles, those would be your primary close range armaments instead of your coil guns.