Equivalent to PDB HETATM records

[tomnewport]

I have some proteins with amino acid ligands. In PDB files these appear in HETATM records (rather than ATOM records), however, I can't find a way to separate them out using the Python MMTF implementation (example structure: http://www.rcsb.org/pdb/explore/explore.do?structureId=4RO2)

[arose]

You can look at groupType.chemCompType.toUpperCase(). In NGL I flag atoms/groups as hetero when it is one of "NON-POLYMER", "OTHER", "D-SACCHARIDE", "D-SACCHARIDE 1,4 AND 1,4 LINKING", "D-SACCHARIDE 1,4 AND 1,6 LINKING", "L-SACCHARIDE", "L-SACCHARIDE 1,4 AND 1,4 LINKING", "L-SACCHARIDE 1,4 AND 1,6 LINKING", "SACCHARIDE".

[tomnewport]

Looking at residue B/201 of 4ro2 in PDB format:

HETATM 2567  N   GLY B 201      53.590  68.132  31.220  1.00 58.60           N  
HETATM 2568  CA  GLY B 201      52.346  67.286  31.263  1.00 62.29           C  
HETATM 2569  C   GLY B 201      51.362  67.617  32.386  1.00 65.31           C  
HETATM 2570  O   GLY B 201      50.138  67.618  32.168  1.00 60.95           O  
HETATM 2571  OXT GLY B 201      51.758  67.881  33.536  1.00 64.54           O  

This appears as PEPTIDE LINKING in the MMTF file - I checked NGL and it also gets confused and fails to mark that residue as hetero. In this particular case, the residues are marked as different:

A normal protein polymer GLY looks like this

{
    'bondOrderList': [1, 1, 2], 
    'bondAtomList': [1, 0, 2, 1, 3, 2], 
    'formalChargeList': [0, 0, 0, 0], 
    'atomNameList': ['N', 'CA', 'C', 'O'], 
    'elementList': ['N', 'C', 'C', 'O'], 
    'singleLetterCode': 'G', 
    'chemCompType': 'PEPTIDE LINKING', 
    'groupName': 'GLY'
}

Whilst a hetero GLY looks like this

{
    'bondOrderList': [1, 1, 2, 1], 
    'bondAtomList': [1, 0, 2, 1, 3, 2, 4, 2], 
    'formalChargeList': [0, 0, 0, 0, 0], 
    'atomNameList': ['N', 'CA', 'C', 'O', 'OXT'], 
    'elementList': ['N', 'C', 'C', 'O', 'O'], 
    'singleLetterCode': 'G', 
    'chemCompType': 'PEPTIDE LINKING', 
    'groupName': 'GLY'
}

So, does the MMTF format provide a way to distinguish between these two types of glycines? (I realise my issue might concern the MMTF format rather than the Python implementation of it)

[josemduarte]

You can use the chainIdList (asym_ids in mmCIF files) to know that the GLY in 4ro2 is assigned to a different chain (asym_id) and in turn to a different entity (entity id 3, non-polymeric). That way you can infer that it is an independent molecule and not part of the polypeptide chain B.

In any case in my opinion I think this is misrepresented in the mmCIF file. If the GLY is not peptide-linked, then it should not be called GLY but have another 3-letter identifier.

[arose]

different chain (asym_id) and in turn to a different entity (entity id 3, non-polymeric)

yes, that is how I handle it in NGL, you can see all those lonely GLY with the selection not polymer. I should change my default selection for ball+stick representation to ( hetero or not polymer ) and not ( water or ion ). Thanks for raising this!

In any case in my opinion I think this is misrepresented in the mmCIF file. If the GLY is not peptide-linked, then it should not be called GLY but have another 3-letter identifier.

I think it is ok, the type is PEPTIDE LINKING not peptide linked :)

[tomnewport]

That seems legit - I just wonder if there might be a situation where (for the sake of argument) a tripeptide was modelled in as a ligand.

(I also declare my original question sufficiently addressed if you'd like to close the issue, but it might be interesting to continue discussing)

[pwrose]

Each chemical entity (protein, ligand, etc.) has an entity type: polymer, non-polymer, and water. By checking the entity type, you can determine if it is part of a polymer or non-polymer.

…

On Fri, Jun 9, 2017 at 3:38 AM, Tom Newport ***@***.***> wrote: That seems legit - I just wonder if there might be a situation where (for the sake of argument) a tripeptide was modelled in as a ligand. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#28 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADuwEJrFLWa2QjAbeXk615Yk_6MAZqDeks5sCSCigaJpZM4NyzAJ> .

[tomnewport]

@pwrose good point - I'd forgotten about that record in the file. Will switch to that in due course. Many thanks

[tomnewport]

(I think that probably clears up all the problems I wanted to address - feel free to reopen if needed)