SMTL ID : 6cw6.1

Structure of alpha-GC[8,18] bound by CD1d and in complex with the Va14Vb8.2 TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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.1: 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

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

NAG.2: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: W.23, S.24, N.42 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42

1 x PBS: (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL(Non-covalent)

PBS.4: 20 residues within 4Å: Chain A: Y.73, S.76, F.77, D.80, I.81, L.84, V.118, F.120, W.133, L.150, D.153, G.155, T.156, V.160 Chain C: P.30, N.32, D.95, R.96, G.97 Ligands: PLM.5 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.73, A:F.77, A:F.77, A:I.81, A:L.84, A:V.118, A:F.120, A:W.133, A:W.133 Hydrogen bonds: A:D.80, A:G.155, A:T.156, A:T.156, C:N.32, C:G.97

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 12 residues within 4Å: Chain A: F.10, Q.14, S.28, V.30, W.63, F.70, Y.73, A.102, L.163, C.168, F.171 Ligands: PBS.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.10, A:V.30, A:W.63, A:W.63, A:F.70, A:F.70, A:A.102, A:L.163, A:F.171, A:F.171 Hydrogen bonds: A:S.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., A molecular switch in mouse CD1d modulates natural killer T cell activation by alpha-galactosylsphingamides. J.Biol.Chem. (2019)

Release Date

2019-04-03

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
Chimeric T cell antigen receptor alpha chain: C
Chimeric T cell antigen receptor beta chain Vb8.2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

Chimeric T cell antigen receptor alpha chain

Chimeric T cell antigen receptor beta chain Vb8.2

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