SMTL ID : 3o8x.1

Recognition of Glycolipid Antigen by iNKT Cell TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 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: W.23, S.24, N.42, R.74 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 8 residues within 4Å: Chain A: S.114, F.128, W.129, G.130, T.131, Q.161, L.164, N.165 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.128, A:L.164 Hydrogen bonds: A:S.114, A:S.114, A:G.130

1 x GSL: (2S,3R)-3-HYDROXY-2-(TETRADECANOYLAMINO)OCTADECYL ALPHA-D-GALACTOPYRANOSIDURONIC ACID(Non-covalent)

GSL.3: 22 residues within 4Å: Chain A: Y.73, S.76, F.77, D.80, L.84, V.85, A.102, F.120, W.133, L.143, L.150, D.153, G.155, T.156, T.159, V.160, C.168 Chain C: P.30, N.32, D.95, R.96, G.97 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Y.73, A:F.77, A:F.77, A:L.84, A:V.85, A:A.102, A:F.120, A:W.133, A:L.143, A:L.150, A:T.159, A:V.160 Hydrogen bonds: A:D.80, A:G.155, A:T.156, A:T.156, A:T.156, C:N.32, C:D.95, C:G.97 Water bridges: A:D.153, A:Q.154 Salt bridges: C:R.96

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

NAG.4: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., The V alpha 14 invariant natural killer T cell TCR forces microbial glycolipids and CD1d into a conserved binding mode. J.Exp.Med. (2010)

Release Date

2010-09-29

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
Valpha14 chimera (Mouse variable domain, Human T-cell receptor alpha chain C region constant domain): C
Vbeta8.2 chimera (Mouse variable domain, Human T-cell receptor beta-2 chain C region constant domain): D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

Valpha14 chimera (Mouse variable domain, Human T-cell receptor alpha chain C region constant domain)

Vbeta8.2 chimera (Mouse variable domain, Human T-cell receptor beta-2 chain C region constant domain)

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