Immersive Virtual Reality (iVR) can help students visualise and explore complex chemical concepts, such as protein enzyme structures and interactions. We designed a set of collaborative iVR-based learning tasks on the interaction between a protein enzyme and its substrate. We investigated how 18 pairs (36 students) in undergraduate chemistry courses changed their understanding of enzyme-substrate interactions through iVR learning tasks. Videos of pre- and post-interviews and student-generated diagrams were analysed. Before iVR, students had abstract models of the structure of a protein enzyme or its interaction with a substrate molecule. Over 90 per cent of the students (33/36) explained enzyme-substrate interactions using simplistic lock-and-key diagrams, exclusively focusing on the shape. Although many students employed key scientific terms like activation energy in their explanations, they were unsure how enzymes lowered activation energy or how catalytic reactions occurred. After iVR, all students discussed the inadequacy of 2D diagrams for representing complex enzyme-substrate interactions. About 90 per cent of students (32/36) used concrete ideas such as electron density and orientation of reactants in the active site to explain the probability of successful interactions between the enzyme and its substrate. Our findings provide evidence of how interactive iVR learning tasks can help students explore complex molecular structures, integrate ideas, and build a concrete understanding of challenging science concepts.