SMTL ID : 4y4k.1

Crystal structure of the mCD1d/EF77/iNKTCR ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 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

NAG-NAG-FUC.1: 7 residues within 4Å: Chain A: S.114, F.128, W.129, G.130, 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

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

NAG.2: 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 NAG.3: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 No protein-ligand interaction detected (PLIP)

1 x 49Y: (4Z)-9-[(1R,2R)-2-decylcyclopropyl]-N-[(2S,3S,4S)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]non-4-enamide(Non-covalent)

49Y.4: 28 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, W.63, L.66, M.69, F.70, Y.73, S.76, F.77, D.80, I.81, L.84, L.100, W.133, L.150, D.153, G.155, T.156, V.160, L.163, F.171 Chain C: P.30, N.32, D.95, R.96, G.97 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Q.14, A:V.30, A:W.63, A:L.66, A:F.70, A:F.70, A:Y.73, A:Y.73, A:F.77, A:I.81, A:L.84, A:L.100, A:W.133, A:W.133, A:V.160, A:L.163, A:F.171 Hydrogen bonds: A:D.80, A:G.155, A:T.156, A:T.156, 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 Valpha14Jalpha18 chain (mouse variable, human constant domain): C
chimeric TCR Vbeta8.2 chain (mouse variable, 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 Valpha14Jalpha18 chain (mouse variable, human constant domain)

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

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