Dear Dipankar,
I have had a case where I had soaked the same compound in Trypsin (2.2 Å) and
in Factor Xa (2.0 Å). In Trypsin, one six-membered ring was completely
invisible, despite good resolution and phases, whereas this ring was clearly
visible in the Factor Xa structure. The electron density is shown in J.Med.Chem
(2002)45:2749 figures 1A and 1E.
It does happen that parts of a soaked compound are completely without electron
density. In these cases I assume that this part is disordered and I refine the
compound without the undefined parts, while in contrast to flexible surface
residues, people look closely at bound compounds and use the structures e.g. to
optimize scoring functions for docking programs. Leaving the undefined parts in
the model in a guessed conformation would likely cause people to draw wrong
conclusions.
For the rest, if the inhibitor is well-defined in the electron density maps, I
would not worry about the high B factors. They may even normalize once you
leave out the undefined part.
Best regards,
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of
Dipankar Manna
Sent: Wednesday, April 11, 2012 11:11 AM
To: [email protected]
Subject: [ccp4bb] Ligand fitting into density
Dear Crystallographers,
The protein I am working with is having SG P3121, Structure is solved
at 2.5A. the protein was soaked with compound, compound density is also looking
prominent except one six membered ring. There is no density at all for the
particular ring, but other parts of the compound is fitting well enough into
the density. The B factor of the ligand is showing >100. How can I justify this
issue. Asking for suggestions.
Regards,
Dipankar Manna
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