SMTL ID : 6cwb.1

Structure of alpha-GSA[8,4P] 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: 9 residues within 4Å: Chain A: E.113, S.114, F.128, W.129, G.130, T.131, Q.161, L.164, N.165 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.128, 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: 2 residues within 4Å: Chain A: A.19, N.20 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 PLM: PALMITIC ACID(Non-covalent)

PLM.4: 10 residues within 4Å: Chain A: Q.14, S.28, V.30, W.40, I.47, W.63, F.70, A.102, L.163, F.171 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.30, A:I.47, A:W.63, A:F.70, A:A.102, A:F.171, A:F.171 Hydrogen bonds: A:S.28

1 x FJJ: (5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-[(1E)-4-phenylbutylidene]-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide (non-preferred name)(Non-covalent)

FJJ.5: 20 residues within 4Å: Chain A: Y.73, S.76, F.77, D.80, L.84, L.100, F.120, W.133, L.143, L.150, D.153, G.155, T.156, V.160, L.163 Chain C: P.30, N.32, D.95, R.96, G.97 18 PLIP interactions: 3 interactions with chain C, 15 interactions with chain A Hydrogen bonds: C:N.32, C:R.96, C:G.97, A:Y.73, A:G.155, A:T.156, A:T.156 Hydrophobic interactions: A:Y.73, A:Y.73, A:Y.73, A:F.77, A:L.84, A:L.100, A:F.120, A:L.143, A:L.150, A:V.160, A:L.163

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 6 residues within 4Å: Chain D: R.37, Q.38, D.39, H.42, G.43, R.45 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.39, D:D.39, D:R.45, D:R.45, D:R.45

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 Va14,Va24,Ja18: C
Chimeric T cell antigen receptor beta chain Vb8.2, vb11: 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 Va14,Va24,Ja18

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

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