Hi, Why is it that you are so reluctant to identify this compound as Ser-Gly? Its fit to the density is great.
To wax historical, we saw unexpected density in the active site of "apo" Thermolysin. It appeared to be Val-Ala, but with refinement it developed into Val-Lys. It happens that Val-Lys are the last two residues of the protein. Residues 315 and 316 were present at full occupancy in the crystal so I presume the peptide was clipped off molecules that didn't crystallize. Of course proving that the density actually represents Ser-Gly, or any other compound you decide upon is much harder than building a model to fit the density. What is harder than identifying a bit of density, is coming up with an experiment to prove it. Dale Tronrud Ronaldo Alves Pinto Nagem wrote:
Dear CCP4bb users, As suggested by some users, I am attaching to this email the electron density of the unidentified ligand. As I mentioned before it looks like a dipeptide GlySer, but we are still in doubt. Attempts to correlate with the protein function are being done. One might see in the pictures that the ligand coordinate a metal ion. Cheers Ronaldo. --------------------------------------------------------- Prof. Dr. Ronaldo Alves Pinto Nagem Universidade Federal de Minas Gerais Instituto de Ciências Biológicas Departamento de Bioquímica e Imunologia Av. Antônio Carlos, 6627 - Caixa Postal 486 Bairro Pampulha - CEP: 31270-901 Belo Horizonte, MG - Brasil Tel: +55 31 3499-2626 Fax: +55 31 3499-2614 E-mail: [EMAIL PROTECTED] ------------------------------------------------------------------------ ------------------------------------------------------------------------
