I have two enzymes, with heme cofactors. but their overall structure is very different.

I use Pymol regularly to visualize protein pdb structures.

I want to align both structures, but the structures don't align well due to very low homology. However, their active sites/substrate entrance channels may be more similar than the rest of the structure. so,

  1. I want to align only the substrate channels from both enzymes and compare their structure. or
  2. align both proteins only using the heme as a reference point. So both hemes from two enzymes align and then I can manually do the rest.

I am more interested in how the substrate would be accessible in both enzymes differently.

Thanks in advance.

Edit: Sorry for being a bit unclear. We can pick two proteins like cytochrome P450 BM3 with pdb id 6H1L or 6H1O. The second protein can be a similar peroxygenase UPO, e.g. 7pn4. Thanks.

  • $\begingroup$ @terdon , do the same rules of SO apply to Bioinformatics , the question seems too wide , at least irfan could have named two pdbs code as inputs, toghrther with the aa defining the channels to have us to try to get a result with $\endgroup$
    – pippo1980
    Commented Sep 27, 2023 at 9:26
  • $\begingroup$ If you feel the question is too broad, then ask for clarifications and/or vote to close as "needs more focus". That said, I don't see why this is too broad: the main question here is "given two pdb structures, how can I align and compare only specific parts of those structures instead?" which seems like it should be answerable by those working with this kind of data. $\endgroup$
    – terdon
    Commented Sep 27, 2023 at 9:33
  • 1
    $\begingroup$ Please add more context to this question; be as specific as possible about the problem you're struggling with. Example proteins, or other input files, are very helpful. $\endgroup$
    – gringer
    Commented Sep 28, 2023 at 3:13

1 Answer 1


OK, trying to answer question 2, think I need to be sure that both enzymes have same identical heme cofactor and then find a rotation/translation matrix that applied to heme of protein A moved exactly on top of heme of protein B , than I have to move the entire protein backbone of protein A using that matrix, is it reasonable ? Am I getting it wrong ? With PyMOL I tried to use Pair/Pair_fit command with two heme proteins : 2d0t https://www.rcsb.org/structure/2d0t and 4zv8 (https://www.rcsb.org/structure/4ZV8) :

pair hem_2d0t , hem_4zv8, same as pair_fit hem_2d0t , hem_4zv8, where hem_2d0t,hem_4zv8 are the heme of the two proteins [select model 2d0t and resn HEM and set_name sele, hem_2d0t or select hem_2d0t, model 2d0t and resn HEM].

See results, superposed heme:

enter image description here

Superposed Proteins :

enter image description here

As for question 1 I tried to answer using the tools available to me. I picked the two same proteins : 2d0t (https://www.rcsb.org/structure/2d0t and 4zv8 (https://www.rcsb.org/structure/4ZV8). Using parKVFinder (https://github.com/LBC-LNBio/parKVFinder , https://www.softxjournal.com/article/S2352-7110(20)30319-8/fulltext) pymol plugin on both proteins stripped of all their HETATM, I calculated their cavities. As an example , here a png of 2d0t cavities :

enter image description here

Then I extracted the residues surrounding the cavity using :

select model 2d0t_merged near_to 5.0 of resn KAF ; [named sele_2d0t]

select model 4zv8_merged near_to 5.0 of resn KAB ; [named sele_4zv8]

being KAF and KAB cavities described as non_bounded atom in pdb format as output of parKVFinder .
I believe parKVFinder has its own output for the residues surrounding cavities, but wanted to try PyMOL

Example for 2d0t :

enter image description here

Then I used

cealign sele_4zv8 , sele_2d0t (https://pymolwiki.org/index.php/Cealign) to align the residues of the two cavities. (cealign uses just CA of the selections provided).

Results , only cavities and surrounding residues :

enter image description here

the two heme protein cavities are not alignrd even if the HIS (2dt0, red) and CYS (4zv8, yellow) are on the same side :

enter image description here


2dt0 in magenta

4zv8 in cyan

I choose 2 different heme protein (could be more extreme though) , just because the question was open to broad attempts, could be interesting too see for example results on not too distant cytochromes

  • $\begingroup$ Thank you very much. I will try to follow the process and report back. $\endgroup$
    – Irfan
    Commented Oct 2, 2023 at 16:02

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