SMTL ID : 5vcj.1

Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.16 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-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

1 x N57: (2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl alpha-D-galactopyranoside(Non-covalent)

N57.2: 18 residues within 4Å: Chain A: Y.73, S.76, F.77, D.80, I.81, L.84, V.118, F.120, W.133, L.150, D.153, G.155, T.156 Chain C: P.30, N.32, R.96, G.97 Ligands: PLM.3 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.73, A:Y.73, A:F.77, A:F.77, A:I.81, A:L.84, A:L.84, A:V.118, A:W.133, A:L.150 Hydrogen bonds: A:D.80, A:G.155, A:T.156, C:N.32, C:G.97

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.3: 12 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, I.47, F.70, Y.73, L.100, T.156, V.160, L.163 Ligands: N57.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.30, A:I.47, A:F.70, A:F.70, A:F.70, A:Y.73, A:Y.73, A:V.160, A:L.163

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

NAG.4: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: W.23, S.24, N.42 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Compton, B.J. et al., Enhancing T cell responses and tumour immunity by vaccination with peptides conjugated to a weak NKT cell agonist. Org. Biomol. Chem. (2019)

Release Date

2018-04-04

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain): C
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain): 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 TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)

Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)

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