Maybe I missed it - but was there any explanation of the type of matter or structure it has?
It's described in the book as
a set of free-floating instructions designed to adapt to and guide other replicating systems
So, it's kind of like a virus or even more like a computer virus. That makes it substrate-independent. In other words, just information.
It's semi-sentient, replicating, shape-shifting handwavium that's been created by an ancient alien life-form. Abaddon's Gate has the most interaction with the protomolecule substance so far in the series of books.
The background behind it's purpose and origin isn't really explored to any real depth other than having the characters deal with it.
Alien, non-human lifeform that absorbs all kinds of energy including nuclear and seeks to overtake any other organisms by transforming them and learning from them. A captured body is not killed but rather infected and modified to accommodate the protomolecule mass. It learns from a captured body and computers too by accessing and processing all memories and information. A captured entity becomes one with the protomolecule which operates as a single being and consciousness unless a part is separated and taken away.