SMTL ID : 6e7d.1 (1 other biounit)

Structure of the inhibitory NKR-P1B receptor bound to the host-encoded ligand, Clr-b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-8-4-mer

Ligands

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

SO4.1: 2 residues within 4Å: Chain B: R.92 Chain J: N.27 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain J Salt bridges: B:R.92 Hydrogen bonds: J:N.27 SO4.3: 5 residues within 4Å: Chain H: R.109 Chain I: H.21, S.23, Q.24, V.25 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:Q.24, I:V.25 Salt bridges: I:H.21, I:K.39, H:R.109 SO4.5: 5 residues within 4Å: Chain F: R.109 Chain J: H.21, S.23, Q.24, V.25 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain F Hydrogen bonds: J:V.22, J:Q.24, J:V.25 Salt bridges: J:H.21, F:R.109 SO4.7: 6 residues within 4Å: Chain D: R.109 Chain K: H.21, S.23, Q.24, V.25, K.39 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain D Hydrogen bonds: K:Q.24, K:V.25 Salt bridges: K:H.21, K:K.39, D:R.109 SO4.9: 6 residues within 4Å: Chain C: R.109 Chain L: H.21, V.22, S.23, Q.24, V.25 6 PLIP interactions: 5 interactions with chain L, 1 interactions with chain C Hydrogen bonds: L:Q.24, L:Q.24, L:V.25, C:R.109 Salt bridges: L:H.21, L:K.39

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

NAG.2: 5 residues within 4Å: Chain I: L.45, I.46, W.81, N.83, T.85 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:T.85 Hydrogen bonds: I:I.46, I:T.85, I:T.85 NAG.4: 5 residues within 4Å: Chain J: L.45, I.46, W.81, N.83, T.85 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:T.85 Hydrogen bonds: J:I.46, J:T.85 NAG.6: 5 residues within 4Å: Chain K: L.45, I.46, W.81, N.83, T.85 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:I.46, K:T.85 NAG.8: 5 residues within 4Å: Chain L: L.45, I.46, W.81, N.83, T.85 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:T.85 Hydrogen bonds: L:I.46, L:T.85, L:T.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balaji, G.R. et al., Recognition of host Clr-b by the inhibitory NKR-P1B receptor provides a basis for missing-self recognition. Nat Commun (2018)

Release Date

2018-10-24

Peptides

C-type lectin domain family 2 member D: ABCDEFGH
Killer cell lectin-like receptor subfamily B member 1B allele B: IJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

D
F

E
I

F
J

G
O

H
P

I
Q

J
S

K
U

L
X

C-type lectin domain family 2 member D

Killer cell lectin-like receptor subfamily B member 1B allele B

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