SMTL ID : 3scm.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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: 5 residues within 4Å: Chain A: W.129, G.130, T.131, Q.161, N.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.129

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

NAG.2: 3 residues within 4Å: Chain A: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP) NAG.3: 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

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

LGN.4: 32 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, I.47, L.66, F.70, Y.73, S.76, F.77, D.80, L.84, V.85, A.102, W.133, W.142, D.153, G.155, T.156, T.159, V.160, M.162, C.168, F.171 Chain C: P.28, D.29, N.30, V.50, K.67, R.94, G.95 24 PLIP interactions: 20 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.10, A:V.30, A:I.47, A:L.66, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:F.77, A:L.84, A:V.85, A:A.102, A:W.142, A:T.156, A:T.159, A:F.171 Hydrogen bonds: A:T.156, A:T.156, A:T.159, A:T.159, C:N.30, C:N.30, C:K.67, C:G.95

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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