SMTL ID : 3o9w.1

Recognition of a Glycolipid Antigen by the iNKT Cell TCR

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: 5 residues within 4Å: Chain A: W.23, S.24, R.25, N.42, D.43 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: E.113, S.114, W.129, G.130, T.131, Q.161, L.164, N.165 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.164 Hydrogen bonds: A:S.114, A:S.114, A:G.130

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

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

1 x 1O2: (2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate(Non-covalent)

1O2.4: 28 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, M.69, F.70, Y.73, S.76, F.77, D.80, L.84, V.85, V.118, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, T.159, L.163, F.171 Chain C: P.30, N.32, R.96, G.97 25 PLIP interactions: 21 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Q.14, A:V.30, A:F.70, A:F.70, A:Y.73, A:F.77, A:F.77, A:L.84, A:V.85, A:V.118, A:V.118, A:F.120, A:W.133, A:W.142, A:L.143, A:T.159, A:F.171 Hydrogen bonds: A:D.153, A:G.155, A:T.156, A:T.156, C:N.32, C:G.97 Water bridges: C:N.32, C:K.69

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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