SMTL ID : 4y4f.2 (1 other biounit)

Crystal structure of the mCD1d/GCK127/iNKTCR ternary complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.19 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: 5 residues within 4Å: Chain A: W.129, G.130, T.131, Q.161, N.165 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.23, A:R.25 Hydrogen bonds: A:S.24

1 x 49M: (1R)-1,5-anhydro-1-[(1E,3S,4S,5R)-4,5-dihydroxy-3-(nonacosanoylamino)nonadec-1-en-1-yl]-D-galactitol(Non-covalent)

49M.3: 33 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, I.47, W.63, F.70, Y.73, S.76, F.77, D.80, L.100, A.102, G.103, L.116, V.118, F.120, W.133, L.143, L.150, D.153, G.155, T.156, V.160, L.163, L.164, C.168, F.171 Chain C: P.30, N.32, D.95, R.96, G.97 33 PLIP interactions: 30 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Q.14, A:V.30, A:W.63, A:W.63, A:F.70, A:F.70, A:Y.73, A:Y.73, A:F.77, A:L.100, A:A.102, A:L.116, A:V.118, A:F.120, A:W.133, A:W.133, A:L.143, A:L.150, A:T.156, A:V.160, A:L.163, A:L.164, A:L.164, A:F.171 Hydrogen bonds: A:D.80, A:D.153, A:G.155, A:T.156, A:T.156, A:T.156, C:N.32, C:R.96, C:G.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Birkholz, A. et al., Structural modifications of alphaGalCer in both lipid and carbohydrate moiety influence activation of murine and human iNKT cells. To Be Published

Release Date

2015-05-27

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
E

B
F

C
G

D
H

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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