SMTL ID : 3sda.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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: 3 residues within 4Å: Chain A: G.130, 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: A.19, N.20, S.22, W.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20 NAG.3: 2 residues within 4Å: Chain A: R.25, N.42 No protein-ligand interaction detected (PLIP)

1 x GCY: N-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosanamide(Non-covalent)

GCY.4: 23 residues within 4Å: Chain A: Q.14, S.28, V.30, I.47, M.69, F.70, Y.73, S.76, F.77, D.80, L.84, F.120, W.133, W.142, L.143, L.150, D.153, T.156, T.159, V.160 Chain C: P.28, N.30, G.95 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.30, A:I.47, A:F.70, A:F.70, A:Y.73, A:Y.73, A:F.77, A:L.84, A:L.84, A:F.120, A:W.133, A:W.142, A:L.143, A:L.150, A:T.156, A:V.160 Hydrogen bonds: A:D.80, A:T.156, A:T.156, C:N.30, C:G.95

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: R.11, W.31 Chain B: S.55, F.56, S.57, Y.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.55

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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