SMTL ID : 3quz.1

Structure of the mouse CD1d-NU-alpha-GalCer-iNKT TCR complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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(Post Translational Modification)

NAG-NAG-FUC.1: 7 residues within 4Å: Chain A: E.113, S.114, 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:T.26, A:R.74

1 x QUV: N-[(2S,3S,4R)-1-({6-deoxy-6-[(naphthalen-1-ylcarbamoyl)amino]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide(Non-covalent)

QUV.4: 34 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, W.40, I.47, W.63, L.66, M.69, F.70, Y.73, S.76, F.77, D.80, I.81, L.100, A.102, V.118, W.133, L.143, L.150, D.153, G.155, T.156, T.159, V.160, L.163, C.168, F.171 Chain C: P.30, N.32, D.95, R.96, G.97 40 PLIP interactions: 36 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Q.14, A:V.30, A:W.40, A:I.47, A:W.63, A:L.66, A:L.66, A:M.69, A:F.70, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:Y.73, A:I.81, A:L.100, A:A.102, A:V.118, A:W.133, A:L.143, A:T.159, A:T.159, A:V.160, A:L.163, A:F.171, A:F.171 Hydrogen bonds: A:D.153, A:G.155, A:T.156, A:T.156, C:N.32, C:R.96, C:G.97 Water bridges: A:Y.73, A:S.76, A:Q.154, A:T.156, A:T.156, C:N.32 pi-Stacking: A:F.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aspeslagh, S. et al., Galactose-modified iNKT cell agonists stabilized by an induced fit of CD1d prevent tumour metastasis. Embo J. (2011)

Release Date

2011-06-29

Peptides

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

Valpha14 (mouse variable domain, human constant domain)

Vbeta8.2 (mouse variable domain, human constant domain)

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