SMTL ID : 6cx9.1

Structure of alpha-GSA[16,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:R.74, A:R.74, A:R.74

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

NA.4: 1 residues within 4Å: Chain A: D.144 No protein-ligand interaction detected (PLIP) NA.5: 7 residues within 4Å: Chain A: E.97, I.98, Q.99, A.119, F.120, Q.121, G.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.99, A:Q.99, A:G.122 NA.7: 5 residues within 4Å: Chain A: R.79, D.80, E.83 Chain C: R.96, L.100 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.79, A:R.79, A:D.80, C:R.96 NA.8: 3 residues within 4Å: Chain C: T.141 Chain D: T.140, R.193 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.140, C:T.141 NA.9: 6 residues within 4Å: Chain C: Q.7, S.8, L.22, Q.23, W.36, T.109 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.7, C:S.8, C:Q.23, C:Q.23 NA.10: 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 NA.11: 4 residues within 4Å: Chain D: P.150, H.152, F.212, Y.213 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.150, D:H.152, D:Y.213

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)

EM4.6: 29 residues within 4Å: Chain A: L.66, Y.73, S.76, F.77, D.80, I.81, L.84, V.85, I.98, L.100, A.102, L.116, F.120, W.133, W.142, L.143, P.146, L.150, D.153, G.155, T.156, V.160, C.168, F.171 Chain C: P.30, N.32, D.95, R.96, G.97 27 PLIP interactions: 23 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.66, A:Y.73, A:Y.73, A:I.81, A:L.84, A:V.85, A:I.98, A:L.100, A:A.102, A:L.116, A:F.120, A:F.120, A:W.142, A:P.146, A:L.150, A:V.160, A:F.171 Hydrogen bonds: A:Y.73, A:G.155, A:T.156, A:T.156, C:N.32, C:R.96, C:G.97 Water bridges: A:Y.73, A:Q.154, C: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

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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