SMTL ID : 6e7d.2 (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

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

NAG.1: 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.3: 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.5: 5 residues within 4Å: Chain K: L.45, I.46, W.81, N.83, T.85 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:T.85 Hydrogen bonds: K:I.46, K:T.85 NAG.7: 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

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

SO4.2: 6 residues within 4Å: Chain H: R.109 Chain I: H.21, S.23, Q.24, V.25, K.39 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 SO4.4: 5 residues within 4Å: Chain F: R.109 Chain J: H.21, S.23, Q.24, V.25 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain F Hydrogen bonds: J:Q.24, J:V.25 Salt bridges: J:H.21, F:R.109 SO4.6: 5 residues within 4Å: Chain D: R.109 Chain K: H.21, S.23, Q.24, V.25 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain K Salt bridges: D:R.109, K:H.21 Hydrogen bonds: K:Q.24, K:Q.24, K:V.25 SO4.8: 5 residues within 4Å: Chain L: H.21, S.23, Q.24, V.25, K.39 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:Q.24, L:V.25 Salt bridges: L:H.21, L:K.39

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
B

B
C

C
G

D
H

E
K

F
L

G
M

H
N

I
R

J
T

K
V

L
W

C-type lectin domain family 2 member D

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

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