Good (?) afternoon,
I can't resist quoting the facetious answer, once given to me in a similar
situation by the dear departed Felix Frolow: '*proteins are bastards*'.
Well to be exact he used a much less socially acceptable term, and he said
it in Russian - but the point is that sometimes (most of
Thank you all for responses. I have added my reply below.
On 26 October 2016 at 17:02, Eleanor Dodson wrote:
> Are your 3 crystals isomorphous, and do they all refine well?
Yes, all C2221 crystal datasets refine to ~ 19/23 %
> I guess you struck lucky with DS3 - as suggested it could be a differ
Fiorentino
Sent: 26 October 2016 13:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ligand binding and crystal form
Hello all,
I just solved a NCS-tetrameric (biological assembly is just a dimer) crystal
structures with ligand soak (same plate - same conditions). No density for
ligand is observed in
What is the height of non-origin Patterson function peak for your data sets?
C-centered cells:
216.5 345.8 145.290.090.090.0
and
147.0 354.3 217.490.090.090.0
are very different; however, they have common subgroup F222 with similar
unit cell parameters. In F
Are your 3 crystals isomorphous, and do they all refine well?
I guess you struck lucky with DS3 - as suggested it could be a different
soaking, different crystal size, etc, etc..
If isomorphous I would compare all 3 structures in COOT and look for subtle
differences..
Your C222 and C2221 cells a
Are these three crystals in order of harvesting (with different soaking times)?
How big is your ligand. How accessible is the binding pocket (and is there a
clear difference in accessibility between chains)?
T
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University
Hi Valentina,
> I just solved a NCS-tetrameric (biological assembly is just a dimer) crystal
> structures with ligand soak (same plate - same conditions). No density for
> ligand is observed in the first map. In the 2nd, I have 1 ligand bound. In
> the 3rd, I have 2 ligands bound. Is there any
Dear Veronica,
with 1st, 2nd, 3rd map you mean the density for the same dataset after
three consecutive cycles of building-refining or three different maps from
three different crystals?
If it's the first case, it could be fine, it may mean that at each cycle
you improve the map so you see signal
Hello all,
I just solved a NCS-tetrameric (biological assembly is just a dimer)
crystal structures with ligand soak (same plate - same conditions). No
density for ligand is observed in the first map. In the 2nd, I have 1
ligand bound. In the 3rd, I have 2 ligands bound. Is there any reason for
this
ehalf Of *
> L
> *Sent:* Monday, October 14, 2013 4:53 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Ligand binding protein partner search
>
> ** **
>
> Hi all,
>
> ** **
>
> I'm looking for a way to find/predict protein partner(s) for our ligand
>
will return PDB entries with ligands that
are chemically similar to your ligand.
Peter Rose,
RCSB PDB
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of L
Sent: Monday, October 14, 2013 4:53 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Ligand binding protein partner search
Hi
It's definitely possible to rig, say, autodock to run the same small
molecule over every protein in the PDB. Results, of course, should be
taken with a grain of salt.
On Mon, 2013-10-14 at 20:53 +0900, L wrote:
> Hi all,
>
>
> I'm looking for a way to find/predict protein partner(s) for our
> l
Hi all,
I'm looking for a way to find/predict protein partner(s) for our ligand
(small chemical; MW<500 Da).
There're lots of servers and softwares to find/predict a ligand with known
protein structure, but hardly find a way to discover potential protein
partner(s) with known ligand.
That would
Oakley
Sent: Tuesday, January 13, 2009 1:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ligand binding in multiple conformation
I had a question about flexibility in ligand binding in an enzyme
active site.
Is it possible for a substrate/product analogue to bind in more than
:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ligand binding in multiple conformation
>I had a question about flexibility in ligand binding in an enzyme
active site.
>Is it possible for a substrate/product analogue to bind in more than
one conformation in the active site.
Yes.
Quite precise occupancy.
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Aaron
Oakley
Sent: Monday, January 12, 2009 4:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ligand binding in multiple conformation
>I had a question ab
>I had a question about flexibility in ligand binding in an enzyme active site.
>Is it possible for a substrate/product analogue to bind in more than one
>conformation in the active site.
Yes. It is even possible for portions of a ligand to be disordered and not
discernable in electron densit
hi
yes this may happen in some circumstanceshave a look at
J Am Chem Soc. 2008 Oct 15;130(41):13514-5.
> Hi,
>
> I had a question about flexibility in ligand binding in an enzyme active
> site. Is it possible for a substrate/product analogue to bind in more
> than
> one conformation in the
Hi Mariah,
We have had one case of this, with two partially overlapping conformations
of a ligand, which is not yet published.
Model in both ligand conformations. Then edit the PDB to give them the same
Chain ID, but with alternative conformations for each atom, or each one that
is different. Yo
Hi,
I had a question about flexibility in ligand binding in an enzyme active
site. Is it possible for a substrate/product analogue to bind in more than
one conformation in the active site. Since the ligand/enzyme interactions
are very specific I am a little confused about this.
Also which progra
Rajan Pillai wrote:
Can this problem arise due to loss of isomorphism in the crystals
after soaking with the substrate? The c-axis dimension increased by
~10 angstroms
Yes.
-James Holton
MAD Scientist
Hi All,
I want to confirm the binding of the substrate in the active site of the
enzyme by soaking crystals of the apo-protein with the substrate. I
generated a Fobs_lig - Fobs_apo difference electron density map. Inspection
of the map did not show the characteristic electron density of the
substr
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