You can pdbsum to find the active site of the protein/enzyme. The following link directs you to a tool called pdbsum. This website gives you something called lig-plot which illustrates the ligand with which the protein has been crystallized) bound to the active site. You just need to plug in the pdb id. You can make a note of the amino acids present in the active site and target them during docking. Hope this helps.

http://www.ebi.ac.uk/pdbsum/

http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=4mx2&template=ligands.html&l=1.1

Hi Arushdeep,

  There are several tools available that can predict the catalytic residues in 3-D structures deposited in PDB. The most commonly used tool is "catalytic site atlas" and is available at http://www.ebi.ac.uk/thornton-srv/databases/CSA/ ( you can find the primary citation for this server at http://www.ncbi.nlm.nih.gov/pubmed/14681376). Another useful server is COFACTOR that does structure-based prediction of catalytic residues and it is from the Zhang Lab available at http://zhanglab.ccmb.med.umich.edu/COFACTOR/help.html (the primary citation for this server can be found at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394312/). As regards to prediction of well-characterized enzymes like adenylosuccinate lyase, their active sites are well documented and can be easily determined. To begin with, you can refer to my publication:

https://www.researchgate.net/publication/23708308_Elucidation_of_the_substrate_specificity_kinetic_and_catalytic_mechanism_of_adenylosuccinate_lyase_from_Plasmodium_falciparum

Article Elucidation of the substrate specificity, kinetic and cataly...

You may also try CASTp server available at http://sts.bioe.uic.edu/castp/

You may also try discovery studio visualizer it will also give you the co-ordinates of the active site which will be important for setting up docking parameter file. Hope this helps

Regards