Docking result not same as reference structure

HADDOCK
1

Hi. I am using easy inteface to do docking to dock my protein structure (tubulin) with small ligand (taxol). The PDB i used is IJFF.

First, i extract the chain B and cut the taxol ligand and save as two new PDB file using discovery studio. Then, for the active residue i just input the residue number based on the amino acid residue involved in interaction just as listed in PDBSum. (https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1jff&template=ligands.html&l=3.1)

That is Chain b: 23,26,27,233,236,369,360,370,276,275,274,230,229,292,278. For passive residue,i just tick the define automatically.

However, from the result i get. ( http://milou.science.uu.nl/serviceresults/HADDOCK2.2/3101966852/1jff )
All the structure from the two cluster do not match with my reference structure in residue number interaction using ligplot.

image

May i know what is possible the mistake i have done. Is it because of the wrong active residue of input? Would appreciate if anyone can kindly advice and explain.

2

So basically you want to reproduce the crystal structure from its separated components? (I.e. a bound docking experiment).

Please have a look at the recommended settings for protein-ligand docking on our tutorial web page. And in particular refer to stage2 (setting up a new docking run targeting the identified binding pocket).

Docking has its limitations and there is no warranty you will get exactly the same structure. And taxol is a rather large and complex molecule.
Further you should always analyse multiple solutions/clusters.