SMTL ID : 5mgr.1

Human receptor NKR-P1 in glycosylated form, extracellular domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 10 residues within 4Å: Chain A: L.45, I.46, R.47, D.48, W.81, N.83, S.85, L.87, N.88, D.91 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.88, A:R.47, A:R.47, A:N.88, A:N.88 Water bridges: A:R.47 Hydrophobic interactions: A:W.81, A:L.87

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 10 residues within 4Å: Chain B: L.45, I.46, R.47, W.81, N.83, S.85, L.87, N.88, S.89, D.91 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.91, B:R.47, B:R.47, B:N.88 Hydrophobic interactions: B:W.81, B:L.87 Water bridges: B:N.88, B:N.88

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

NAG.3: 5 residues within 4Å: Chain A: N.30, N.31, A.34 Chain B: N.71, S.73 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.34 Hydrogen bonds: A:N.30, A:N.31, B:N.71, B:S.73 Water bridges: B:L.74, B:L.74 NAG.4: 7 residues within 4Å: Chain A: N.71, S.73, S.75, K.80 Chain B: N.30, N.31, A.34 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.34 Hydrogen bonds: B:N.30, B:N.31, A:N.71, A:S.73, A:K.80, A:K.80 Water bridges: A:L.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blaha, J. et al., Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse. Nat Commun (2022)

Release Date

2018-06-06

Peptides

Killer cell lectin-like receptor subfamily B member 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Killer cell lectin-like receptor subfamily B member 1

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