SMTL ID : 4elm.1 (1 other biounit)

Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.48 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 11 residues within 4Å: Chain A: W.129, G.130, T.131, Q.161, M.162, N.165 Chain C: Y.33, F.52, S.53, D.54, G.55 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.54

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

NAG.2: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.22, A:S.22 NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.23, A:R.25 Hydrogen bonds: A:S.24, A:N.42

1 x SGF: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside(Non-covalent)

SGF.4: 17 residues within 4Å: Chain A: Y.73, S.76, F.77, D.80, L.84, V.118, F.120, W.133, W.142, L.143, L.150, D.153, T.156 Chain D: H.30, F.97, W.98, F.105 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.73, A:L.84, A:V.118, A:F.120, A:F.120, A:W.133, A:W.142, A:W.142, A:L.143, A:L.150 Hydrogen bonds: A:S.76, A:S.76, A:T.156, A:T.156 Salt bridges: D:H.30

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 9 residues within 4Å: Chain A: F.10, C.12, L.66, F.70, L.100, A.102, L.116, L.163, F.171 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.10, A:L.66, A:F.70, A:F.70, A:L.116, A:L.163, A:F.171, A:F.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Girardi, E. et al., Type II natural killer T cells use features of both innate-like and conventional T cells to recognize sulfatide self antigens. Nat.Immunol. (2012)

Release Date

2012-07-25

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2 microglobulin: B
Hy19.3 TCR alpha chain (mouse variable domain, human constant domain): C
Hy19.3 TCR beta chain (mouse variable domain, human constant domain): D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

D
H

Antigen-presenting glycoprotein CD1d1

Beta-2 microglobulin

Hy19.3 TCR alpha chain (mouse variable domain, human constant domain)

Hy19.3 TCR beta chain (mouse variable domain, human constant domain)

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