SMTL ID : 5mgt.1 (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: 5 residues within 4Å: Chain A: N.27, S.30, Y.109 Ligands: SO4.3, SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.109 Hydrogen bonds: A:N.27, A:S.30 NAG.2: 5 residues within 4Å: Chain A: Q.44, E.46, W.77, N.79, T.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.79, A:T.81 NAG.5: 5 residues within 4Å: Chain B: N.27, S.30, Y.109 Ligands: SO4.7, SO4.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.27, B:S.30 Water bridges: B:S.30 NAG.6: 5 residues within 4Å: Chain B: Q.44, E.46, W.77, N.79, T.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.46, B:N.79

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

SO4.3: 4 residues within 4Å: Chain A: K.26, S.30, R.33 Ligands: NAG.1 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.26, A:R.33 SO4.4: 3 residues within 4Å: Chain A: T.29, R.33 Ligands: NAG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.29 Salt bridges: A:R.33 SO4.7: 4 residues within 4Å: Chain B: K.26, S.30, R.33 Ligands: NAG.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.30 Water bridges: B:S.30 Salt bridges: B:K.26, B:R.33 SO4.8: 3 residues within 4Å: Chain B: T.29, R.33 Ligands: NAG.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.29, B:T.29 Salt bridges: B:R.33

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

C-type lectin domain family 2 member D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C-type lectin domain family 2 member D

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