Essentially all of it. Alphafold won't tell you anything about protein dynamics, side-chain positions, water interactions, charges, binding pockets or induced conformational changes. All of these things matter as much or more than the structure of the backbone itself.
One way to think about it is this: alphafold gives you the rough shape of the skeleton, but a protein, just a like a human, has a lot more going on than just the skeleton.
Surprisingly little. Maybe things like binding pockets and broad classes of movement (hinges, etc.) can be inferred (sometimes). Otherwise, it's the other way around: the shape of the backbone is determined by the detailed interactions. Just think about alpha helices and beta sheets -- they're stabilized by hydrogen bonding patterns along the protein backbone, but the propensity of a particular residue to form a helix or a sheet is determined by interactions amongst the side-chain atoms in a particular context. The atomic interactions are the story, and the "fold" is really just the outline.
Also, of course, it's not just the atoms in the protein itself: add in water, ions, small molecules, other proteins, etc., and you have a real mess. A small molecule (say, a drug), can displace a water molecule, which has a cost, which causes something else to move a bit to compensate, stretching a bond, and so on and so forth, sometimes resulting in dramatic differences in the bound conformation of a protein. It's not uncommon -- it's essentially the norm. And it's not like there's just one conformation. The whole thing is really like a wiggly, jiggly, metastable mass, and the introduction of a slight perturbation is enough to send the blob spiraling into a new metastable state.
When you start to ask questions about how a protein moves over time, it becomes a much more complicated problem than predicting the overall conformation. Which is itself quite hard.
One way to think about it is this: alphafold gives you the rough shape of the skeleton, but a protein, just a like a human, has a lot more going on than just the skeleton.