[3dem] Seeking guidance regarding fitting a small molecule ligand to a protein , using a cryoEM map

[Sagnik Sen]

Hi Daniel,

Thanks for the inputs. Basically there are two copies of the ligand , one
each bound to either of the chains of the main protein dimer. Each copy has
one covalent bond that it forms with the respective Cysteine in each chain.

I am going through the linked paper.

I have some experience with using ISOLDE and will try generating the
combined parameters and using them.

Thanks again for your help.

Regards,
Sagnik

On Wed, Oct 15, 2025 at 6:19 PM Daniel Asarnow <dasarnow at gmail.com> wrote:

> Hi Sagnik,
> Are there two copies of the molecule/does it have two reactive moieties?
> Or is it a case where you see both in superposition in the map but each
> copy only has one covalent bond formed?
>
> If the latter you may find this paper interesting.
> https://urldefense.com/v3/__https://www.science.org/doi/full/10.1126/science.aaw2922__;!!Mih3wA!EPr9bsh-mo7H1dU0NiOgzw9fXM2vy4lcIcRoWP4E0iE3K2_oFhthlczBboQHS_f_m4k5pilI2cGf8X3scQ$ 
> <https://urldefense.com/v3/__https://www.science.org/doi/full/10.1126/science.aaw2922__;!!IKRxdwAv5BmarQ!bwMVJRtzlZtnyQhA-s7uAcXqW29v66BdL_MN3JxES3g7dzbVH4j7YWIbA5qWrWMMrvv0fOV3bU3e_vGZa1s$>
>
> To supplement Dom's reply, you can also use those elbow parameters with
> ISOLDE in ChimeraX and use the ISOLDE > Model building > Make bond action
> to create a new bond. Though you may need to generate parameters for a
> combined residue along the lines of e.g. P1L (palmitocysteine) to continue
> the simulation.
>
> Best,
> -da
>
> On Wed, Oct 15, 2025 at 8:20 AM Sagnik Sen via 3dem <3dem at ncmir.ucsd.edu>
> wrote:
>
>> Dear all,
>>
>> We have a sample where a small molecule ligand is bound to a homodimer
>> protein. It forms covalent bonds with the Sulfur of a Cysteine on both the
>> chains. We currently have a cryoEM map of 2.5 Å and we can clearly see
>> the ligand density on both the chains, after fitting the protein model to
>> the map.
>>
>> We are also able to roughly fit the ligand using Coot but seek inputs
>> with respect to forming the bond. Placement of the ligand in the density
>> near to the Cysteine and doing real space refinement does not make the
>> bond.
>>
>> We do have a PDB and restraints file for the ligand, made using Phenix
>> eLBOW. Do we need to edit the PDB files for both the protein and the ligand
>> to make the link? IF so, what is a good way to do that?
>>
>> Or is there a way to fit this using Phenix?
>>
>> Thanks and best regards,
>> Sagnik
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>> <https://urldefense.com/v3/__https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem__;!!IKRxdwAv5BmarQ!bwMVJRtzlZtnyQhA-s7uAcXqW29v66BdL_MN3JxES3g7dzbVH4j7YWIbA5qWrWMMrvv0fOV3bU3eHOt0qAs$>
>>
>
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