SMTL ID : 3sdd.1

Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-beta-lactosylceramide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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: 4 residues within 4Å: Chain A: G.130, T.131, Q.161, N.165 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.24, A:R.25 NAG.3: 2 residues within 4Å: Chain A: N.20, W.23 No protein-ligand interaction detected (PLIP)

1 x 3GD: N-[(2S,3R,4E)-1-{[4-O-(beta-D-galactopyranosyl)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]docosanamide(Non-covalent)

3GD.4: 34 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, I.47, F.70, Y.73, S.76, F.77, D.80, L.84, V.85, L.100, A.102, L.116, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, T.159, V.160, L.163, F.171 Chain C: P.28, N.30, V.50, K.67, R.94, G.95 34 PLIP interactions: 4 interactions with chain C, 30 interactions with chain A Hydrogen bonds: C:N.30, C:V.50, C:K.67, C:G.95, A:D.80, A:D.80, A:T.156, A:T.156, A:T.159 Hydrophobic interactions: A:F.10, A:Q.14, A:V.30, A:I.47, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:F.77, A:F.77, A:L.84, A:V.85, A:L.100, A:A.102, A:L.116, A:F.120, A:W.133, A:W.142, A:L.143, A:L.150, A:T.156, A:V.160, A:L.163, A:F.171, A:F.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pellicci, D.G. et al., Recognition of beta-linked self glycolipids mediated by natural killer T cell antigen receptors. Nat.Immunol. (2011)

Release Date

2011-10-05

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
NKT TCR Valpha14 chain: C
NKT TCR autoreactive-Vbeta6 chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

NKT TCR Valpha14 chain

NKT TCR autoreactive-Vbeta6 chain

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