SMTL ID : 6cw9.1

Structure of alpha-GC[8,16P] bound by CD1d and in complex with the Va14Vb8.2 TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 3 residues within 4Å: Chain C: W.18, S.19, N.37 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: 7 residues within 4Å: Chain C: S.109, W.124, G.125, T.126, Q.156, L.159, N.160 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.159 Hydrogen bonds: C:S.109, C:S.109, C:G.125

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

NAG.3: 4 residues within 4Å: Chain C: A.14, N.15, S.17, W.18 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.15, C:N.15

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.4: 13 residues within 4Å: Chain C: F.5, Q.9, S.23, V.25, W.35, W.58, L.61, F.65, Y.68, A.97, L.158, C.163, F.166 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.5, C:V.25, C:W.58, C:L.61, C:F.65, C:F.65, C:A.97, C:L.158, C:F.166, C:F.166 Hydrogen bonds: C:S.23

1 x 7LM: N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxy-16-phenylhexadecan-2-yl]octanamide(Non-covalent)

7LM.5: 23 residues within 4Å: Chain A: P.28, N.30, D.93, R.94, G.95 Chain C: V.67, Y.68, S.71, F.72, D.75, L.79, V.80, F.115, W.128, W.137, L.138, P.141, L.145, D.148, G.150, T.151, T.154, V.155 24 PLIP interactions: 4 interactions with chain A, 20 interactions with chain C Hydrogen bonds: A:N.30, A:R.94, A:G.95, C:D.148, C:G.150, C:T.151, C:T.151 Water bridges: A:D.29, C:Y.68, C:D.148, C:Q.149, C:T.151 Hydrophobic interactions: C:Y.68, C:L.79, C:V.80, C:F.115, C:F.115, C:W.128, C:W.128, C:W.137, C:P.141, C:L.145, C:T.154, C:V.155

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

Chimeric T cell antigen receptor alpha chain. Va14,Va24,Ja18: A
Chimeric T cell antigen receptor beta chain Vb8.2, vb11: B
Antigen-presenting glycoprotein CD1d1: C
Beta-2-microglobulin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

D
B

Chimeric T cell antigen receptor alpha chain. Va14,Va24,Ja18

Chimeric T cell antigen receptor beta chain Vb8.2, vb11

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin