Iron-Sulfur Cluster in Arsenite Oxidase


#1

Dear All,
I am interested to do the protein-protein docking of Arsenite oxidase with FES cluster and Cytochorome oxidase. We tried several times by changing the iron charges, iron numbering, etc. However we could not able to succeed at inputing the file. My protein four FE atoms and six sulfur atoms. Iam looking forward your kind response to fix this issue.

Please find the error related to this:

"There was an inconsistency in your data

Error message

Second pdb file contains multiple forms of the same residue. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble
ATOM 6647 1FE+2 F3S A2005 -3.573 -48.017 47.906 1.00 55.12 M Fe"

Thanks in advance

Sincerely
Filipa


#2

Hi Filipa

The only supported iron cluster is with two FE and four Sulphur atoms:

CFE: CYS with an iron sulfur cluster. 
HADDOCK will automatically search for closeby CYF residues and created bonds with the iron cluster 
Atoms: 
N,HN,CA,HA,CB,HB1,HB2,SG,FE1,SF1,FE2,SF2,C,O

The list of supported modified amino acids can be found at: https://milou.science.uu.nl/services/HADDOCK2.2/library.html

You might try to define it as HETATM, but each atom must have a unique name.
Also from your PDB it seems you have multiple occupancies for the iron cluster