SMTL ID : 6cx7.1

Structure of alpha-GSA[12,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 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: 6 residues within 4Å: Chain C: S.114, W.129, G.130, T.131, Q.161, N.165 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.114, C:S.114, C:G.130

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

NA.2: 6 residues within 4Å: Chain A: Q.7, S.8, L.22, Q.23, W.36, T.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.7, A:S.8, A:Q.23, A:T.109 NA.3: 6 residues within 4Å: Chain A: D.121, A.123, Y.125, D.142 Chain B: H.135, T.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.121 NA.4: 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:R.37, B:D.39, B:D.39, B:R.45, B:R.45 NA.5: 6 residues within 4Å: Chain B: W.158, V.159, N.160, G.161, H.205, R.207 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.160, B:G.161, B:H.205 NA.10: 7 residues within 4Å: Chain C: E.97, I.98, Q.99, A.119, F.120, Q.121, G.122 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.99, C:A.119, C:G.122

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.6: 13 residues within 4Å: Chain C: F.10, Q.14, S.28, V.30, W.40, L.66, F.70, Y.73, L.163, L.164, C.168, F.171 Ligands: ELM.9 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.10, C:V.30, C:L.66, C:F.70, C:L.163, C:L.164, C:F.171, C:F.171 Hydrogen bonds: C:S.28

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

NAG.7: 3 residues within 4Å: Chain C: A.19, N.20, S.22 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain C: W.23, S.24, N.42 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.23 Hydrogen bonds: C:S.24, C:N.42

1 x ELM: 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)tetra hydro-2H-pyran-2-yl]oxy}octan-2-yl]dodecanamide(Non-covalent)

ELM.9: 26 residues within 4Å: Chain A: P.30, N.32, D.95, R.96, G.97 Chain C: C.12, Q.14, Y.73, S.76, F.77, D.80, I.81, L.84, I.98, L.100, F.120, W.133, W.142, P.146, L.150, D.153, G.155, T.156, T.159, V.160 Ligands: PLM.6 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.73, C:F.77, C:I.81, C:L.84, C:I.98, C:F.120, C:F.120, C:W.142, C:P.146, C:L.150, C:T.159, C:V.160 Hydrogen bonds: C:Y.73, C:D.80, C:D.153, C:G.155, C:T.156, C:T.156, A:N.32, A:G.97

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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