You can try building the model based on secondary structure similarities with
Modeller. www.salilab.org

or any other modelling software.

--- You wrote:
 Hello,

Can anyone suggest a program to construct a 3D structure of one protein
sequence, that has demonstrated low homology with crystal structure in 
current databases?

 Sincerely
 
 Luciani Tatsch Piemolini
 
--- end of quote ---