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]


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