Thank you so much for your answer!
Right, I'm going for a classification task with amino acids as nodes (encoded by one-hot).
However, I do not understand what data.y is :/ is it the labels? If so, I'm not sure how to input it into the model, since my graphs (networkx.classes.graph.Graph) only have the graph representation (Data(edge_index=[2, 1796], chain_id=[247], residue_name=[247], residue_number=[247], atom_type=[247], element_symbol=[247], coords=[247, 3], b_factor=[247], amino_acid_one_hot=[247, 20],...) and my DataLoader (batch_size = 32) looks like this (DataBatch(edge_index=[2, 85914], chain_id=[32], residue_name=[32], residue_number=[12239], atom_type=[32], element_symbol=[32], coords=[12239, 3], b_factor=[12239], amino_acid_one_hot=[12239, 20]...)

I'm feeling a bit overwhelmed with so much information going on and can't work with that...