SMTL ID : 9e6y.1

Structure of CD112 (Nectin-2) domain 1 bound to CD112R (PVRIG)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: P.42, D.43, N.106, M.122 No protein-ligand interaction detected (PLIP) EDO.2: 6 residues within 4Å: Chain A: L.32, I.34, A.87, E.88, L.89, Q.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.34, A:L.89, A:Q.90 EDO.3: 4 residues within 4Å: Chain A: F.54, A.77, K.78, Q.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.79 EDO.4: 4 residues within 4Å: Chain A: P.27, P.28, V.29, L.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.29 EDO.5: 6 residues within 4Å: Chain A: S.69, E.70, R.71, L.72, S.73, H.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.69 EDO.6: 5 residues within 4Å: Chain A: R.41, D.43, G.105, N.106, W.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.106, A:N.106 Water bridges: A:R.41, A:R.41 EDO.8: 5 residues within 4Å: Chain A: Q.40, Q.49 Chain B: S.103, W.104, E.105 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.105, B:E.105 Water bridges: A:Q.49 EDO.9: 3 residues within 4Å: Chain B: T.70, Q.71 Ligands: EDO.10 No protein-ligand interaction detected (PLIP) EDO.10: 7 residues within 4Å: Chain B: W.68, E.69, Q.71, S.72, S.73 Ligands: EDO.9, EDO.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.72, B:S.73, B:S.73 EDO.11: 3 residues within 4Å: Chain B: P.53, W.68 Ligands: EDO.10 No protein-ligand interaction detected (PLIP) EDO.12: 1 residues within 4Å: Chain B: T.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.1

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 1 residues within 4Å: Chain B: N.89 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S. et al., Structure-guided engineering of CD112 receptor variants for optimized immunotherapy. Mol.Ther. (2025)

Release Date

2025-05-07

Peptides

Nectin-2: A
Transmembrane protein PVRIG: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

Nectin-2

Transmembrane protein PVRIG