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The organization of the cellular interior gives rise to properties including metabolic channeling and micro-compartmentalization of signaling. Here, we use a lattice model of molecular crowding, together with literature-derived protein interactions and abundances, to describe the molecular organization and stoichiometry of local cellular regions, showing that physical protein–protein interactions induce emergent structures not seen when random interaction networks are modeled. Specifically, we find that the lattices give rise to micro-groups of enzymes on the surfaces of protein clusters. These arrangements of proteins are also robust to protein overexpression, while still showing evidence for expression tuning. Our results indicate that some of the complex organization of the cell may derive from simple rules of molecular aggregation and interaction.We use a lattice model of cells' interior to describe the organization of local regions, showing that protein-protein interactions give rise to emergent structures. For instance, the lattices contain micro-groups of enzymes on protein cluster surfaces. These lattices are also robust to over-expression. We suggest that some of the cell's organization derives from simple rules of aggregation and interaction.