Dear Wei,
It seems that coot detects some discrepancies between cif file and your
ligand. It is not uncommon that the program used to generate your ligand
pdb produces atom definitions that are not correctly read by programs
used to generate restrains, such as PRODRG. In order to overcome the
Dear Jan,
since electrostatics go with one over distance-square, there may still be some
electrostatic repulsion if the aspartic acid is further away as the arginine.
Another question is, what happens with the arginine of the ligand in absence of
the antibody? Does it then make a salt bridge
Hi all,
I would like to write CCP4 or .xplor maps of a potential field I have derived
myself.
I am using python and have a 3D grid of floating points. I would like to write
these out as a ccp4 or .xplor map.
Does anybody have any suggestions of functions that might be able to help me
with
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Anthony,
xplor maps are ascii format and you can write them easily with
'printf' (I guess this function is available in python). You can find
the format description with any qualified search engine like ixquick
or duckduckgo etc.
Best,
Tim
On
Hi Anthony,
You can achieve this easily using the cctbx. I assume that your 3D grid of
floating points is a numpy array - if so you will have to convert this to a
cctbx flex array as shown in the simple example below. The cctbx can also has
the functionality to write out xplor maps - if needed
Dear colleagues,
We have two full professorship positions in Biochemistry to fill
(permanent positions, salary level W3). People with a research focus in
any field of molecular/mechanistic biochemistry are welcome.
Job duties include teaching also at the Bachelor level, which is being
done in
Dear Jan,
Is there a possibility for bifurcated salt bridges/H-bonds where the Asp
would be entrapped between the two arginines, in which case, repulsive
effects would not take place ?
Cheers,
Nadir Mrabet
Pr. Nadir T. Mrabet
Structural Molecular Biochemistry
N-gere - INSERM U-954
Hi Jan,
please note, Arg-Arg proximity is not always repulsive: guanidinium groups can
associate bridged by H-bonds and interactions with water molecules or
neighboring amino acids. There are many examples of these unusual Arg
formations, see for reference:
Neves, Yeager and Abagyan (2012)
Thanks for your responses,
Andrey, I had no idea about these arginine associations. In this case
the arginines are facing each other guanidinium to guanidinium. I
guess they wouldn't attract. Nadir, the asp is not entrapped between
the two arginines. But Hermann is probably right by saying that
Yes, indeed Andrey.
And this results from resonance (tautomerization) of the guanidinium group.
Regards,
Nadir Mrabet
Pr. Nadir T. Mrabet
Structural Molecular Biochemistry
N-gere - INSERM U-954
University of Lorraine, Nancy
School of Sciences and Technologies
School of Medicine
9, Avenue de
Jan,
Ionic interaction does reduce the charges born by the partners in isolation.
This is why charged residues found in the protein core are always paired.
Furthermore, concerning arg, beyond the fact that they are found to
autointeract as Andrey pointed out, the charge they bear is spread over
An example of pi-pi stacking of the guanidinium groups, can be seen on a
structure which I worked on; pdb-code: 2x2u. Look at the interactions
between Arg 77 and its symmetry mate, with Arg 144 (and symmetry copy)
flanking, giving rise to a stack of 4 Arginine guanidinium groups, with
a sulphate
Dear all,
I would to acknowledge everyone that replied to my post, both privately and to
the BB, for the very useful comments and suggestions. Here is my conclusion so
far:
Taking into consideration especially the planarity resulting from the presence
of double bonds, it seems that indeed there
Yes, the two arginines are from two different models. One has the antibody and
the other one the ligand. But if you imagine that both are bound to the
receptor, asp still can't be entrapped between the arginines.
And if the asp was entrapped between the two arginine it would also mean that
the
We are trying to apply this approach for the first time to define a
crystallizable domain of our protein of interest. Can anyone send a
protocol that includes exactly how to do the mass spectrometry
measurement? Our core lab here doesn't know and I'm just not that gifted.
Happy October, G
A post-doctoral position is immediately available in the Skordalakes laboratory
at The Wistar Institute UPENN to study protein Nucleic acid assemblies that
participate in the replication and maintenance of telomeres. We are looking for
highly motivated candidates that have recently acquired a
In 3U9C we observed even 6 arginines (residues A278, A280 and A306
plus symmetry mates of chain B) mediating a crystalline contact by
pi/pi stacking. We called this motif an arginine zipper
(see Fig. 5 in dx.doi.org/10.1107/S0907444912016587).
Karsten Niefind
An example of pi-pi stacking
Dear all,
I am sorry for a non-ccp4 question. Does any one know of a server/program
which can be used to draw the secondary structure elements e.g. If I
specify 1-50 loop, 51-100 helix, 101-120 loop...like that...I have
secondary structure prediction for the sequence, but for presentation which
Hello,
I am working with a metalloenzyme and was looking for ICP-MS capability in
Boston area to determine metal identity of my protein. Currently I am
sending samples to UNC and was hoping to get access to such a facility
locally.
Sinecerly,
Aditi
Pro-Origami ?
pdbsum ?
Ashu Kumar wrote:
Dear all,
I am sorry for a non-ccp4 question. Does any one know of a server/program which
can be
used to draw the secondary structure elements e.g. If I specify 1-50 loop,
51-100 helix,
101-120 loop...like that...I have secondary structure prediction
No, my mistake, those require a structure.
If you have only sequence and predictions, I think TopDraw would be ideal.
Edward A. Berry wrote:
Pro-Origami ?
pdbsum ?
Ashu Kumar wrote:
Dear all,
I am sorry for a non-ccp4 question. Does any one know of a server/program which
can be
used to
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