SMTL ID : 8ea8.1

NKG2D complexed with inhibitor 4a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 7 residues within 4Å: Chain A: Y.65, I.95, A.106, S.107, K.110, Y.112 Ligands: PGE.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.107, A:K.110, A:Y.112 PGE.2: 7 residues within 4Å: Chain A: K.53, N.90, L.91, L.92, T.93, S.108, F.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.53, A:T.93 Water bridges: A:K.53 PGE.5: 1 residues within 4Å: Ligands: PGE.1 No protein-ligand interaction detected (PLIP) PGE.6: 3 residues within 4Å: Chain B: M.97, Q.98, K.99 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.99, B:K.99 PGE.7: 9 residues within 4Å: Chain A: Y.19, D.57, L.58, K.60, L.61 Chain B: N.15, I.17, Q.25, F.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.26 PGE.9: 7 residues within 4Å: Chain B: K.53, N.90, L.91, L.92, T.93, S.108, F.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.53, B:T.93 Water bridges: B:K.60

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 7 residues within 4Å: Chain A: N.15, Q.25, F.26 Chain B: Y.19, D.57, L.58, L.61 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:D.57 Hydrogen bonds: A:N.15, A:F.26, A:F.26 PEG.8: 4 residues within 4Å: Chain A: E.6 Chain B: G.10, P.11, R.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.6

1 x VML: N-{(1S)-2-(dimethylamino)-2-oxo-1-[3-(trifluoromethyl)phenyl]ethyl}-4-[4-(trifluoromethyl)phenyl]pyridine-3-carboxamide(Non-covalent)

VML.4: 15 residues within 4Å: Chain A: I.17, F.26, L.61, V.62, K.63, H.66 Chain B: I.17, Y.24, Q.25, F.26, L.58, L.61, V.62, K.63, I.123 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.26, A:L.61, A:V.62, B:F.26, B:F.26, B:I.123 Hydrogen bonds: A:L.61, A:K.63, B:K.63 pi-Stacking: B:F.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, A.A. et al., Identification of small-molecule protein-protein interaction inhibitors for NKG2D. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-05-03

Peptides

NKG2-D type II integral membrane protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

NKG2-D type II integral membrane protein

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