SMTL ID : 6bnl.1 (1 other biounit)

Crystal structure of TCR-MHC-like molecule

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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 No protein-ligand interaction detected (PLIP)

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 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.20 NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.23, A:R.25 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:R.25, A:R.25

1 x QWV: N-[(2S,3R)-3-hydroxy-1-{[6-O-(3-phenylpropanoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide(Non-covalent)

QWV.4: 36 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, I.47, W.63, M.69, F.70, Y.73, S.76, F.77, D.80, L.100, A.102, V.118, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, T.159, V.160, M.162, L.163, L.164, C.168, F.171 Chain C: P.28, N.30, D.93, R.94, G.95 35 PLIP interactions: 31 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.10, A:Q.14, A:V.30, A:I.47, A:W.63, A:M.69, A:F.70, A:F.70, A:Y.73, A:Y.73, A:F.77, A:F.77, A:L.100, A:A.102, A:V.118, A:F.120, A:W.133, A:W.142, A:L.143, A:L.150, A:L.150, A:T.159, A:V.160, A:L.163, A:L.164, A:F.171 Hydrogen bonds: A:D.153, A:G.155, A:T.156, A:T.156, C:N.30, C:R.94, C:G.95 Water bridges: A:D.153 Salt bridges: C:R.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chennamadhavuni, D. et al., Dual Modifications of alpha-Galactosylceramide Synergize to Promote Activation of Human Invariant Natural Killer T Cells and Stimulate Anti-tumor Immunity. Cell Chem Biol (2018)

Release Date

2018-04-04

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains: C
NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains: 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 Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains

NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains

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