SMTL ID : 4y16.1

Crystal structure of the mCD1d/NC-aGC/iNKTCR ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUL.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 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 48G: N-[(2S,3S,4R)-3,4-dihydroxy-1-{[6-O-(naphthalen-1-ylcarbamoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide(Non-covalent)

48G.3: 37 residues within 4Å: Chain A: F.10, 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.84, L.100, A.102, G.103, V.118, F.120, W.133, W.142, L.150, D.153, G.155, T.156, T.159, V.160, L.163, F.171 Chain C: P.30, N.32, D.95, R.96, G.97 37 PLIP interactions: 32 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:F.10, A:F.10, A:W.40, A:I.47, A:W.63, A:L.66, A:M.69, A:F.70, A:Y.73, A:Y.73, A:F.77, A:I.81, A:L.84, A:L.100, A:V.118, A:F.120, A:W.133, A:W.142, A:T.156, A:T.159, A:V.160, A:L.163, A:F.171, A:F.171 Hydrogen bonds: A:D.80, A:D.153, A:G.155, A:T.156, A:T.156, A:T.156, A:T.159, C:N.32, C:R.96, C:G.97 pi-Stacking: A:F.70 Water bridges: C:D.31, C:D.31

1 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)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Birkholz, A. et al., Lipid and Carbohydrate Modifications of alpha-Galactosylceramide Differently Influence Mouse and Human Type I Natural Killer T Cell Activation. J.Biol.Chem. (2015)

Release Date

2015-06-03

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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