SMTL ID : 8tm2.1

Preclinical Characterization of Pan-NKG2D Ligand-Binding NKG2D Receptor Decoys

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain B: R.6, N.8, E.25, Q.91, I.93, Y.111 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.82, Q.86, G.90 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: I.208, N.211, S.213 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: K.105, G.106, N.121 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.105 Hydrogen bonds: A:S.123 NAG.5: 3 residues within 4Å: Chain A: N.50, Q.136, P.138 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain B: N.102, R.169 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.169

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: K.116 Chain B: R.94, D.163 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.116, A:K.116, B:R.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rupert, P.B. et al., Preclinical characterization of Pan-NKG2D ligand-binding NKG2D receptor decoys. Heliyon (2024)

Release Date

2024-04-17

Peptides

NKG2-D type II integral membrane protein: A
MHC class I polypeptide-related sequence A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

NKG2-D type II integral membrane protein

MHC class I polypeptide-related sequence A

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