SMTL ID : 3ta3.1

Structure of the mouse CD1d-Glc-DAG-s2-iNKT TCR complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 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, R.25, N.42 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(Post Translational Modification)

NAG-NAG-FUC.2: 7 residues within 4Å: Chain A: S.114, F.128, W.129, G.130, T.131, Q.161, N.165 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.128 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 3TF: (2S)-1-(alpha-D-glucopyranosyloxy)-3-(hexadecanoyloxy)propan-2-yl (11Z)-octadec-11-enoate(Non-covalent)

3TF.4: 28 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, I.47, F.70, Y.73, S.76, F.77, D.80, L.84, V.85, E.92, L.100, V.118, F.120, W.133, L.143, L.150, D.153, G.155, T.156, T.159, L.163 Chain C: P.30, N.32, R.96, G.97 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:V.30, A:I.47, A:Y.73, A:Y.73, A:Y.73, A:F.77, A:F.77, A:L.84, A:V.85, A:E.92, A:L.100, A:V.118, A:F.120, A:F.120, A:W.133, A:W.133, A:W.133, A:L.143, A:L.163 Hydrogen bonds: A:D.153, A:G.155, A:T.156, A:T.156, A:T.159, C:N.32, C:G.97 Water bridges: C:D.31, C:D.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Girardi, E. et al., Unique Interplay between Sugar and Lipid in Determining the Antigenic Potency of Bacterial Antigens for NKT Cells. Plos Biol. (2011)

Release Date

2011-11-23

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
Valpha14 chimera (mouse variable domain, human constant domain): C
Vbeta8.2 chimera (mouse variable domain, human 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 constant domain)

Vbeta8.2 chimera (mouse variable domain, human constant domain)

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