SMTL ID : 6cxa.1

Structure of alpha-GSA[20,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-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: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, N.42, R.74 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42, A:R.74

1 x EMG: 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]icosanamide(Non-covalent)

EMG.4: 30 residues within 4Å: Chain A: V.30, L.66, F.70, Y.73, S.76, F.77, D.80, L.84, V.85, I.98, A.102, L.116, V.118, F.120, W.133, W.142, P.146, L.150, D.153, G.155, T.156, T.159, V.160, C.168, F.171 Chain C: P.30, N.32, D.95, R.96, G.97 26 PLIP interactions: 3 interactions with chain C, 23 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:V.30, A:L.66, A:F.70, A:Y.73, A:F.77, A:L.84, A:V.85, A:I.98, A:A.102, A:L.116, A:V.118, A:F.120, A:F.120, A:W.142, A:P.146, A:L.150, A:T.159, A:V.160, A:F.171

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

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:A.119, A:G.122 NA.6: 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:S.8, C:Q.23 NA.7: 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:H.152, D:H.152, D:Y.213 NA.8: 6 residues within 4Å: Chain D: W.158, V.159, N.160, G.161, H.205, R.207 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.160, D:G.161, D:H.205

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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