SMTL ID : 5mgt.2 (2 other biounits)

Complex of human NKR-P1 and LLT1 in deglycosylated forms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: L.45, I.46, R.47, W.81, N.83, S.85 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.46, A:R.47, A:S.85, A:S.85 Water bridges: A:R.47, A:N.83, A:N.83 NAG.2: 9 residues within 4Å: Chain A: W.29, N.71, K.80, W.81, I.82, N.101 Chain B: N.30, N.31, A.34 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.30, B:N.30, B:N.31, A:N.71, A:K.80, A:W.81 Water bridges: A:N.71 NAG.4: 5 residues within 4Å: Chain B: L.45, I.46, W.81, N.83, S.85 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.46, B:S.85, B:S.85 Water bridges: B:N.83 NAG.5: 10 residues within 4Å: Chain A: N.30, N.31, A.34 Chain B: W.29, N.71, K.80, I.82, N.101, C.116 Ligands: SO4.6 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.71, B:K.80, A:N.30, A:N.30 Water bridges: B:N.71, B:F.72, B:K.80, B:W.81

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: S.73, L.74, S.75, K.80, F.86 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.74, A:S.75, A:S.75 Salt bridges: A:K.80 SO4.6: 5 residues within 4Å: Chain A: N.31 Chain B: S.73, S.75, K.80 Ligands: NAG.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.73, B:L.74 Salt bridges: B:K.80

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain B: K.62, A.63, S.107, Q.108, T.109 Ligand excluded by PLIP

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
C

B
D

Killer cell lectin-like receptor subfamily B member 1

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