SMTL ID : 6cwe.1

Structure of alpha-GSA[8,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: W.23, S.24, N.42 No protein-ligand interaction detected (PLIP)

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.2: 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 Water bridges: A:T.131 Hydrophobic interactions: A:L.164 Hydrogen bonds: A:S.114, A:S.114, A:G.130

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

NAG.3: 3 residues within 4Å: Chain A: A.19, N.20, W.23 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.20, A:N.20

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

7LP.4: 24 residues within 4Å: Chain A: Y.73, S.76, F.77, D.80, I.81, L.84, I.98, L.100, F.120, W.133, W.142, L.143, P.146, L.150, D.153, G.155, T.156, V.160 Chain C: P.30, N.32, D.95, R.96, G.97 Ligands: PLM.5 24 PLIP interactions: 21 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.73, A:Y.73, A:F.77, A:I.81, A:L.84, A:I.98, A:F.120, A:F.120, A:W.142, A:P.146, A:L.150, A:T.156, A:V.160 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:D.153, A:D.153, A:Q.154

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 13 residues within 4Å: Chain A: Q.14, S.28, V.30, W.40, I.47, W.63, L.66, F.70, A.102, L.163, C.168, F.171 Ligands: 7LP.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.30, A:I.47, A:W.63, A:L.66, A:F.70, A:F.70, A:F.70, A:A.102, A:F.171 Hydrogen bonds: A:S.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Glycolipid recognition by iNKT cells. To Be Published

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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