SMTL ID : 3tvm.2 (1 other biounit)

Structure of the mouse CD1d-SMC124-iNKT TCR complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 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: 4 residues within 4Å: Chain A: W.23, S.24, R.25, 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(Post Translational Modification)

NAG-NAG-FUC.2: 9 residues within 4Å: Chain A: E.113, S.114, F.128, W.129, 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

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, S.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.22

1 x 07P: N-[(2S,3R)-10-[(1R,2R)-2-decylcyclopropyl]-1-(alpha-D-galactopyranosyloxy)-3-hydroxydecan-2-yl]hexacosanamide(Non-covalent)

07P.4: 35 residues within 4Å: Chain A: Q.14, S.28, V.30, W.40, I.47, M.69, F.70, Y.73, S.76, D.80, I.81, L.84, V.85, E.92, I.96, L.100, A.102, V.118, F.120, V.126, W.133, W.142, L.143, L.150, D.153, G.155, T.156, V.160, C.168, F.171 Chain C: P.30, N.32, D.95, R.96, G.97 33 PLIP interactions: 31 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.30, A:W.40, A:I.47, A:F.70, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:I.81, A:L.84, A:V.85, A:E.92, A:I.96, A:L.100, A:A.102, A:V.118, A:F.120, A:F.120, A:F.120, A:V.126, A:W.133, A:W.133, A:W.142, A:L.143, A:L.150, A:V.160, A:F.171 Hydrogen bonds: A:D.80, A:G.155, A:T.156, A:T.156, C:N.32, C:G.97

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: T.37, H.38, F.49, T.50, K.51, P.52, W.53, S.54, Q.55 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.50, A:T.50, A:K.51, A:S.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tyznik, A.J. et al., Glycolipids that Elicit IFN-gama-Biased Responses from Natural Killer T Cells. Chem.Biol. (2011)

Release Date

2012-02-01

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
E

B
F

C
G

D
H

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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