Re: [ccp4bb] Putting ligand in the protein structure

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

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- X-ray detectors

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: to extract protein sequence from a rebuilt pdb file
From: Jane Bailey jbailey {- dot -} xtal {- at -} GOOGLEMAIL {- dot -} COM
Date: 2008-10-01

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Subject: Re: Putting ligand in the protein structure
From: Scott Pegan pegan {- at -} UIC {- dot -} EDU
Date: 2008-10-01

Subject: Re: Putting ligand in the protein structure
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-10-01

On Sep 30, 2008, at 9:56, Anshul Awasthi wrote:

> Hi all the crystallographers,
>
> I am trying to solve a structure of a protein with some inhibitor. I
> want to
> know how I can put in my inhibitor in the density map of the data i
> got. I
> can see some density in the active site where the inhibitor should
> be. I
> generated the topoly file of the inhibitor (in both pdba nd refmac5
> top
> formats) from the Dundee PRODRG server. Now do i need to incorporate
> the
> structure of the inhibitor in ccp4 or can i do in coot?? I am not
> sure of
> how to do it.

As one of many alternatives you can use "ARP/wARP Ligand Fit" from
the CCP4I
(provided you downloaded and installed the current version of ARP/wARP)
and then input your protein structure, the observed data, and the PDB
of your ligand.

The script will calculate the mFo-DFc map, find the most likely site
for the ligand,
and then fir the ligand there, and refine it in real space.

Tassos

>
>
> ANy sugegstion will be very valuable for me.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: to extract protein sequence from a rebuilt pdb file
From: Jane Bailey jbailey {- dot -} xtal {- at -} GOOGLEMAIL {- dot -} COM
Date: 2008-10-01

Next message:
Subject: Re: Putting ligand in the protein structure
From: Scott Pegan pegan {- at -} UIC {- dot -} EDU
Date: 2008-10-01