Glycoside hydrolase 13 (GH13) family represents a large and diverse enzyme family. Cqm1, an amylomaltase of Culex mosquito, belongs to the GH13 family and subfamily 17 (GH13_17). The protein acts as the receptor for mosquito-larvicidal BinAB toxin that is used world-wide for control of the mosquito population. The protein was crystallized in the presence of a mixture of divalent metal ions. Cqm1 crystal structure was solved using the MRSAD method using Cd(II) anomalous at 1.9 Å wavelength and the structure was refined against 1.8 Å synchrotron data. One tightly bound Ca(II) ion in each of the monomer was observed and this site is suggested here to be unique to the GH13_17 family. Molecular dynamics simulations provide clues for the functional role of Ca(II) ion shown earlier to be essential for enzymatic activity. An optimized substrate (maltotriose) bound structure of the complex was constructed based on which ‘retaining-type’ mechanism can be predicted reliably. It reveals large conformational change in aromatic residues situated at active-site entrance. A Cd(II) ion was observed overlapping with the substrate-binding site. Kinetics data suggests non-competitive inhibition of Cqm1 by Cd(II). This is the first structure from the GH13_17 family and provides template for constructing reliable models for other members.