Look at the publication(s) associated with the specific structure, as well as any other structure of the same protein in the pdb. Usually, a single structure is not sufficient to deduce the conformational changes associated with the mechanism of transport, although any single structure is a useful starting point. There might be a poorly resolved structure available of the transporter without bound antibody to confirm that the structure with the fab is close to the native structure. Functional assays may be used to test whether or not the Fab can bind in the context of the intact membrane, and whether or not it interferes with the function of the transporter. Binding of small molecule substrates and inhibitors may still be able to elicit conformational changes that will, in the corresponding structures, help elicit the transport path and mechanism.

You use all information available to interpret a structure, not only the atom coordinates of one single complex , but correlate these to the results of the biochemical and physiological characterisation of the construct used for structure determination, comparing these to a similar characterisation of the wild-type molecule.