IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes
Fig 14
Comparing IgV-IgV interfaces A-B) CD96 vs.
TIGIT interacting with nectin-like protein-5 (necl-5) (PDBid: 6ARQ, 3UDW) using their N-terminal IgV domain shown side by side with their residue interaction network, using IgStrand numbering. C) Different residue interaction network in CD96 and in TIGIT https://structure.ncbi.nlm.nih.gov/icn3d/share.html?HppETGxGj1yjQ7md7&t=6ARQ,3UDW. D-E) PD-L1 interacting with PD1 (PDBid 4ZQK) vs. PDL1 interacting with a nanobody (PDBid 5JDS) (https://structure.ncbi.nlm.nih.gov/icn3d/share.html?ehLCiHmy953yyGMeA&t=4ZQK,5JDS targeting the same epitope/surface on the PDL1 GFCC’ sheet, using an elaborate FG (CDR3) loop from igs# 8553 to igs# 9547. F) PD1/Nivolumab (PDBid: 5WT9) interaction. Nivolumab binds to a PD1 epitope composed of the FG loop residues as well as an N-terminal loop that is considered outside of the PD1 domain in IgStrand numbering, hence the residues (in cyan)are not numbered and retain their PDB numbers. This points to the need to consider Ig domain extensions. The interface that can be compared to the PD1/PDL1 interface in D) https://structure.ncbi.nlm.nih.gov/icn3d/share.html?UhSpS48KgM7dsMUD8&t=4ZQK,5WT9.