Re: [ccp4bb] ligand binds to one molecule

2022-03-05 Thread Bernhard Rupp
As you stated, you have multiple protomers in the asymmetric unit, where they are free from crystallographic symmetry constraints. Generally that means different local environment for each protomer. Inspecting the sites in the different protomers (frequently related by various

Re: [ccp4bb] ligand binds to one molecule

2022-03-05 Thread zaigham khan
Hey, That is a good question, and there could be multiple reasons. One possibility could be the crystal contacts. I have experience with the pentameric vial surface protein (PMID: 24648448), and I could see the carbohydrate ligand only in a subset of protein chains in ASU. Another reason could

Re: [ccp4bb] ligand binds to one molecule

2022-03-05 Thread Krieger, James M
Perhaps the subunits have different conformational states that are differently able to bind the ligand. There are definitely oligomers where the subunits do that e.g. mGluR1 binding domain dimer is usually 1 open subunit and 1 closed in the active state without cations at the interface. This is

[ccp4bb] ligand binds to one molecule

2022-03-05 Thread
Hello all, In homo-dimeric or homo-oligomeric protein crystal structures, what would be the reason for having a ligand (chemical compound or fragment) binds to one molecule and not all molecules in the asymmetric unit? I have soaked a fragment that has an affinity of 200 uM to a viral protein