Hi all,
I am struggling with coordinating zinc to a zinc finger and failed over 30 times. To check what’s going wrong, I tried to test a PDB deposited structure (PDB ID: 1sp1), Briefly, (1) zinc is removed from the NMR structure1sp1 to generate the protein input file (Chain A), (2) protein is removed from 1sp1 to generate the zinc ion input file (Chain number was changed to D (Chain D)). Both input files were generated using the discovery studio visualizer. Inputting both files to HADDOCK has no error.
Everything on the HADDOCK server was set to default except inputting the unambiguous restrain file (file name: test.tbl) and the contents are as follows.
assign (segid A and resid 5 and name SG)
(segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
assign (segid A and resid 8 and name SG)
(segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
assign (segid A and resid 21 and name NE2)
(segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
assign (segid A and resid 25 and name NE2)
(segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
HADDOCK generated clusters within ~12 hours, but the zinc ion is >10 nm away from the protein binding site. Please see the link below with all the input data I used to generate a complex. I would appreciate it if someone guides me in troubleshooting what is wrong I am doing here or if I am missing something that I need to input.
https://drive.google.com/drive/folders/1684hG6_MbJpqGppBxFi68WAq2EkXg_45?usp=sharing
HADDOCK results are accessible here for your reference
https://wenmr.science.uu.nl/haddock2.4/result/2701304514/250966-1sp1
Best,
Sanjay