SMTL ID : 8t4z.1

T-cell receptor and lipid complex structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: W.23, S.24, N.42, R.74 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: W.129, G.130, T.131, Q.161, N.165 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.129 Hydrogen bonds: A:T.131

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.2: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 No protein-ligand interaction detected (PLIP)

1 x Y73: N-[(2R,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide(Non-covalent)

Y73.4: 26 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, W.40, I.47, W.63, F.70, Y.73, S.76, F.77, D.80, I.81, L.84, V.85, I.98, V.118, W.133, T.156, T.159, V.160, L.163, F.171 Chain C: P.28, R.94 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.10, A:Q.14, A:V.30, A:W.40, A:W.40, A:I.47, A:W.63, A:F.70, A:F.70, A:Y.73, A:F.77, A:F.77, A:I.81, A:V.85, A:I.98, A:V.118, A:V.118, A:W.133, A:V.160, A:F.171, A:F.171 Hydrogen bonds: A:S.76, A:S.76, A:D.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, T.Y. et al., Lipidomic scanning of self-lipids identifies headless antigens for natural killer T cells. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-08-07

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera: C
Beta-chain, T cell receptor beta chain MC.7.G5 chimera: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera

Beta-chain, T cell receptor beta chain MC.7.G5 chimera

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