We developed a coarse grained two-well model to study the single molecule protein conformational dynamics in microscopic detail at the residue level, overcoming the often encountered computational bottleneck. In particular, we explored the underlying conformational energy landscape of adenylate kinase, a crucial protein for signal transduction in the cell, and identified two major kinetic pathways for the conformational switch between open and closed states through either the intermediate state or the transient state. Based on the parameters fitted to the room-temperature experimental data, we predicted open and closed kinetic rates at the whole temperature ranges from 10 to 50 degrees C, which agree well with the experimental turnover numbers. After uncovering the underlying mechanism for conformational dynamics and exploring the structural correlations, we found the crucial dynamical interplay between the nucleoside monophosphate binding domain (NMP) and the ATP-binding domain (LID) in controlling the conformational switch. The key residues and contacts responsible for the conformational transitions are identified by following the time evolution of the two-dimensional spatial contact maps and characterizing the transition state as well as intermediate structure ensembles through phi value analysis. Our model provides a general framework to study the conformational dynamics of biomolecules and can be applied to many other systems.