grafts

A grafts directive is used to specify grafting of a structure onto the main structure. Each graft is expressed as a shortcode string:

<target>:<source>

Target specification

The <target> has the format:

<chain>_<R1>[#<R2>[#<R3>...]]

where <chain> is the chain ID in the base structure and <R1>, <R2>, etc. are residue numbers (with optional insertion codes) that serve as the alignment basis — the residues in the base structure onto which the congruent source residues will be superimposed. Multiple residues are separated by #.

Examples:

  • A_512 — single-residue target: align to residue 512 of chain A

  • G_542#543 — two-residue target: align to residues 542 and 543 of chain G

  • G_572#573#574 — three-residue target: align to residues 572, 573, and 574 of chain G

Source specification

The <source> has the format:

<pdbid>,<chain>_<S1>[#<S2>[#<S3>...]][-<E>]

where <pdbid> is the basename of the PDB file or PDB ID, <chain> is the chain ID in the source PDB, <S1>, <S2>, etc. are the source index residues used for alignment (one per target residue, in the same order), and the optional [-<E>] limits the graft to source residues up to and including <E>.

Rules:

  • The number of source index residues must equal the number of target residues (N), or N+1, in which case the last one is interpreted as source_end.

  • Source residues that are not index residues (and are within the source_end limit if given) are the donor residues that become new atoms in the built structure.

Examples:

  • 4byh,C_1-10 — align to source residue 1, donate residues 2–10

  • 4b7i,C_1#2-8 — align to source residues 1 and 2, donate residues 3–8

  • 4b7i,C_1#2#3-8 — align to source residues 1, 2, and 3, donate residues 4–8

N-point alignment and dihedral pre-conditioning

When more than one alignment residue is specified, pestifer performs N-point alignment with dihedral pre-conditioning.

This is particularly useful for glycan grafting onto structures that already carry a partial glycan stub at the target site. For example, if the base structure already has a two-sugar NAG–NAG stub at an N-glycosylation site, a two-residue target (G_542#543) aligned to congruent two-residue source resids (4b7i,C_1#2-8) will produce a much better placement of the donated sugars than a one-residue alignment.

Pre-conditioning runs before the alignment transformation is computed. For each glycosidic bond between consecutive source index residues (processed innermost-to-outermost):

  1. The target’s phi and psi angles (and omega for 1→6 and 2→6 linkages) are measured in the base structure.

  2. The corresponding angles are measured in the source PDB.

  3. The difference (target − source) is used to rotate the source glycan around the appropriate bond axis, moving the outer (donor) side while keeping the innermost index residue fixed.

After pre-conditioning, the standard measure fit least-squares alignment is applied to all N index residues simultaneously, and the donor residues are transformed accordingly.

Full example

A two-residue graft that extends the NAG–NAG stub at residue 542–543 of chain G with residues 3–8 from PDB 4b7i chain C:

- G_542#543:4b7i,C_1#2-8

And a three-residue graft for a site where the base already has a three-sugar stub (NAG–NAG–BMA at 572–573–574):

- G_572#573#574:4b7i,C_1#2#3-8

A good example of using grafts to fully glycosylate a protein is Example 15: Fully Glycosylated, Closed SARS-CoV-2 Omicron BA.2 Variant Spike.