Experts,
I would like to compare the substrate binding site of two homologous
proteins. Based on crystal structures it is clear that the substrate
binding site of protein A is more solvent exposed then protein B.
Is there a way to measure the solvent exposure of the substrate in protein
A and B?
Hey Jeff,
Why not try the command line version of CAVER. It is easily adjustable and
provides nice figures of solvent accessibility for Pymol. It also prints
out a ton of stats in the log files if you want numbers.
-Yarrow
On Wed, Jun 25, 2014 at 1:10 PM, Jeff Holden wrote:
> Experts,
>
> I w
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jeff
Holden
Gesendet: Mittwoch, 25. Juni 2014 22:11
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] solvent exposed
Experts,
I would like to compare the substrate binding site of two homologous proteins
substrate will give you an estimate of
the solvent exposed surface.
Best regards,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jeff
Holden
Gesendet: Mittwoch, 25. Juni 2014 22:11
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] solve
My structure has a Cys that is solvent-exposed and an unidentified
'blob' of density which is connected to the sulfur of the Cys. The
protein was crystallized in presence of DTT, and DTT does fit the
density. However, I do not know if it is oxidized or not, as the density
does not appear to acc
Thank you for your reply. I don't actually see anything interacting with
what would be the second SH of the DTT. The atom opposite the Cys sulfur
is at a distance of 3.0 A (could this eventually suggest hydrogen
bonding)?? I have been looking at examples in the PDB, and have found a
few protei
Martyn
*From:* Lynn Gregory-Pauron
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Tuesday, 23 June, 2009 9:11:28 AM
*Subject:* Re: [ccp4bb] Solvent-exposed Cys and an unidentified ligand
Thank you for your reply. I don't actual
