[phenixbb] protein-ligand complex structure

Bosch, Juergen jubosch at jhsph.edu
Thu Oct 24 19:31:51 PDT 2013

Hi Wei,
have you considered modeling two conformations of your ligand in the four sites ?

On Oct 24, 2013, at 10:19 PM, Wei Shi wrote:

Hi all,
I am working on a structure of protein-ligand complex. Four ligands are placed for the dimer protein and the density for the two ligands of the first monomer is better than the density for the other two ligands of the second monomer. Ligand is moved to fit density better in Coot (and for two ligands of the first monomer, they fits the density almost perfectly), but after a refinement in phenix (default settings + NCS restraints + Secondary structural restraints + Optimize X-ray/stereochemistry weight +Optimize X-ray/ADP weight), some part of the ligand which fits density good before moved out of the density again...Besides, it always shows green density in Coot for the ligand region even in places where the ligand is in density...
Any suggestions or ideas about how to fit the ligand better and why the density for ligands of the second monomer is worse than that for the first monomer and why the ligands would move out of density after refinement?
Is it because the protein model is not good enough to get the ligand density good? There is a conformational change upon ligand binding, and I rebuilt some part of the protein manually, and the density for a region of about 30 residues is not very good, and I tried to mutate those to alanies and refine, but it didn't help me see the density better...
Any suggestions or ideas on how to improve this protein-complex structural model?  Thank you so much!
The statistics for the current best model is as follows, and the resolution of the dataset is 2.8Å.

                           start         final
  R-work:           0.3359        0.2993
  R-free:             0.3619        0.3558
  RMS(angles):     1.03           1.55
  RMS(bonds):    0.006          0.007

MolProbity validation
Ramachandran outliers:   4.7% (Goal: < 0.2%)
Ramachandran favored:  85.3% (Goal: > 98%)
Rotamer outliers:   4.5% (Goal: 1%)
C-beta outliers:   0    (Goal: 0)
Clashscore:   7.43
Overall score:   2.56

Thank you so much!

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Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:      +1-410-614-4894
Fax:      +1-410-955-2926

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