Peptide Residues Chemical Component Dictionary Remediation

Background information

As of July 2023, the PDB archive has no CCD data items to describe whether an atom within a peptide residue is part of the amino acid backbone or part of the N- or C-terminal groups of the peptide residue. In addition, amino acid CCDs do not yet have standardised atom naming for the backbone atoms, which makes it difficult to identify which atoms form the N- and C-terminal groups.

The Peptide Residues Remediation therefore focuses on addressing the following:

• Adding new CCD data items to label atoms that form the backbone, N- or C-terminal groups
• Standardising the atom naming of peptide backbone atoms

This will ensure that the backbone and terminal atoms are labelled in polypeptide residues, and that backbone atom names are standardised in polypeptide residue CCD files.

Files affected by this remediation

• CCD files
• mmCIF model files
• PRD and PRD-CC files
• NMR chemical shift files, molecular restraints files, NMR combined str files

Example files are available at github: https://github.com/wwPDB/backbone-extension

Adding new CCD data items to label atoms that form the backbone, N- or C-terminal groups

The new CCD data items to flag the backbone and terminal groups of the peptide residues will be stored in three new mmCIF items to the CCD category _chem_comp_atom, as follows:

• pdbx_backbone_flag

Is the atom part of the backbone of the peptide residue?

Accepted values:

Y

N

• pdbx_n_terminal_flag

Is the atom a N-terminal atom in the peptide residue?

Accepted values:

Y

N

• pdbx_c_terminal_flag

Is the atom a C-terminal atom in the peptide residue?

Accepted values:

Y

N

Rules for Backbone Flag

The following rules have been used to populate the backbone flag for all existing backbone atoms:

1. All atoms that lie between the N- and C-terminal groups should be labelled as backbone.
1. This is usually the shortest path between the two but there are exceptions (e.g. chromophores).
2. When the backbone is difficult to identify, it is chosen as the shortest path between the two termini.



2. All hydrogens linked to the backbone atoms are labelled as backbone.
3. All atoms in the backbone carboxyl group are labelled as backbone.
1. O, OXT and HXT
4. Any atoms that are modifications to the backbone are not considered backbone atoms.

Rules for Terminal Atoms

The following rules have been used to populate the N- and C-terminal flags:

1. All atoms in the amino group and carboxyl group are considered terminal atoms.
2. This includes oxygens and all hydrogens on these groups.
1. N-terminal are: N, H, H2
2. C-terminal are: C, O, OXT, HXT
3. In some rare cases, the terminal group is replaced by a very similar group. In these cases, where considered appropriate, the similar group should be labelled as terminal.





4. In cases where the residue can be flipped in the polypeptide sequence, both terminal groups can described as N- and C-terminal. These atoms should be labelled with Y for both terminal group items.
1. For example, some non-standard residues contain two carboxyl or two amino groups rather than the standard peptide backbone (e.g., PX1, see example image in previous section).

Standardising the atom naming of peptide backbone atoms

Rules for Atom Naming

The following rules have been used to update the atom naming of all existing backbone atoms (excluding chromophores and capping residues, see below):

1. The C-terminal linked carboxyl group should always be called C.
2. Where it has the full carboxyl group, the atoms should be called O/OXT/HXT (OXT and HXT being the leaving atoms).
3. The N-terminal linked amino group should always be called N.
1. Where it has one hydrogen only it should be called H.
2. Where it has two hydrogens, they should be called H/H2 (H2 being the leaving atom).
3. Where it has three hydrogens, they should be called H/H2/H3 (H2/H3 being the leaving atoms).
4. The backbone carbon with both an amino group and side chain should be called CA.



5. When a carbon has an amino group, and another carbon has the side chain, then the carbon with the side chain should be CA.



6. No two atoms should have the same atom name.
7. Backbone hydrogen atom naming will not be fully standardised, except H/H2/H3/HXT.

In some cases, side chain atom naming was inconsistent or clashed with the new backbone atom names, and has therefore been updated to align with the new annotation rules.

Additional information

Updates to leaving atom flags

During the remediation process, many CCDs were identified to have missing or incorrect leaving atoms on the backbone. It was particularly common that the N- or C-terminal leaving atoms were not assigned. As part of the remediation, all missing or incorrect leaving atoms on the backbone have been fixed.

Rules for Chromophores

The annotation rules for chromophores and chromophore-like CCDs are slightly different to standard amino acid residues:

1. The N-terminal atoms should be called N1/H/H2.
2. The C-terminal carboxyl atoms should be called C3/O3/OXT/HXT.
3. Where possible, the backbone atom naming should match the CDD CRO.
4. The backbone atoms should be handled in the same way as standard peptides (excluding the shortest path rule).
5. However, it should also include all the atoms involved in the peptide bonds.
6. T6619 132nd Ave NE, Kirkland, WA 98033his means that the oxygens that form the peptide bonds should also be labelled as backbone.



7. The terminal groups should be handled in the same way as standard peptides.
8. The N-terminal group should only be added for the first residue in the chromophore (i.e. on N1 not N2/N3 groups).
9. The C-terminal group should only be added for the last residue in the chromophore (i.e. on C3, not C1/C2 groups).
10. In rare cases, there are 4 not 3 residues in the chromophore. In these cases the atoms should be named:
1. N0, CA0, C0 etc. if the additional residue is on the N-terminus
2. N4, CA4, C4 etc. if the additional residue is on the C-terminus

Rules for Terminal Cap Residues

The annotation rules for N- and C-terminal cap residues CCDs are different to standard amino acid residues. These terminal caps are defined as: “Any CCD that only occurs on either the N- or C-terminal position of polypeptides and that does not have a standard amino acid backbone, but instead has a single group that connects them to the polypeptide sequence. This is usually a carboxyl group for N-terminal caps and an amino group for C-terminal caps.”

The rules for annotating the backbone and terminal flags for these CCDs are:

1. Only the atoms that are part of the group connecting the cap to the polypeptide backbone should be labelled as backbone.
1. For N-terminal caps, this will usually be the carboxyl group atoms.
2. For C-terminal caps, this will usually be the amino group atoms.
2. N-terminal caps have a C-terminal group but not an N-terminal group and so:
1. No atoms should be labelled as being N-terminal.
2. The atoms labelled as backbone should all be labelled as C-terminal.
3. C-terminal caps follow the same format, except they contain an N-terminal group but not a C-terminal group.
4. As these cap residues do not resemble standard amino acids, atom renaming has not been performed for these residues.

Acknowledgements

The peptide residues chemical component dictionary remediation project is part of the protein chemical modifications (PCMs) and post translational modifications (PTMs) remediation project, a wwPDB collaborative project carried out principally by PDBe at EMBL-EBI, and is funded by BBSRC grant number BB/V018779/1.