SMTL ID : 6cxe.1

Structure of alpha-GSA[26,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 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 C: 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 C Hydrophobic interactions: C:F.128, C:L.164 Hydrogen bonds: C:S.114, C:S.114, C:G.130

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

NA.2: 5 residues within 4Å: Chain A: L.100, G.101, R.102 Chain B: Y.51 Chain C: E.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.101 NA.3: 6 residues within 4Å: Chain B: R.37, Q.38, D.39, H.42, G.43, R.45 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.39, B:D.39, B:G.43, B:R.45, B:R.45 NA.4: 6 residues within 4Å: Chain A: A.99 Chain B: Y.34, G.98, Y.99, T.100, Q.101 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.34, B:T.100 Water bridges: B:D.96, B:Q.101 NA.8: 5 residues within 4Å: Chain A: R.96, L.100 Chain C: R.79, D.80, E.83 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.79, C:D.80, A:R.96, A:L.100

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

NAG.5: 3 residues within 4Å: Chain C: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain C: W.23, S.24, N.42 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.23 Hydrogen bonds: C:S.24, C:N.42 Water bridges: C:S.24, C:S.24, C:R.74

1 x EM4: N-[(2S,3S,4R)-3,4-dihydroxy-8-oxo-8-[(6-phenylhexyl)amino]-1-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octan-2-yl]hexacosanamide(Non-covalent)

EM4.7: 37 residues within 4Å: Chain A: P.30, N.32, D.95, R.96, G.97 Chain C: F.10, C.12, Q.14, S.28, V.30, I.47, W.63, L.66, F.70, V.72, Y.73, S.76, F.77, D.80, I.81, L.84, L.100, A.102, L.116, V.118, F.120, W.133, W.142, L.143, P.146, L.150, D.153, G.155, T.156, T.159, V.160, F.171 34 PLIP interactions: 29 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:F.10, C:F.10, C:V.30, C:I.47, C:W.63, C:L.66, C:F.70, C:Y.73, C:Y.73, C:Y.73, C:I.81, C:L.84, C:L.100, C:A.102, C:L.116, C:F.120, C:W.142, C:P.146, C:L.150, C:T.159, C:V.160, C:F.171 Hydrogen bonds: C:Y.73, C:G.155, C:T.156, C:T.156, A:N.32, A:R.96, A:G.97 Water bridges: C:D.153, C:Q.154, C:T.156, A:D.31, A:K.69

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

2019-04-10

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

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