SMTL ID : 3arg.1

Ternary crystal structure of the mouse NKT TCR-CD1d-alpha-glucosylceramide(C20:2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 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: 2 residues within 4Å: Chain A: N.20, W.23 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: G.130, Q.161, N.165 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.24

1 x DB6: (11E,14E)-N-[(2S,3S,4R)-1-(alpha-D-glucopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide(Non-covalent)

DB6.4: 24 residues within 4Å: Chain A: C.12, Q.14, S.28, M.69, F.70, Y.73, S.76, F.77, D.80, I.81, L.84, V.118, F.120, W.133, D.153, G.155, T.156, T.159, V.160, F.171 Chain C: P.28, N.30, R.94, G.95 26 PLIP interactions: 4 interactions with chain C, 22 interactions with chain A Hydrogen bonds: C:N.30, C:R.94, C:R.94, C:G.95, A:D.153, A:G.155, A:T.156, A:T.156, A:T.156 Hydrophobic interactions: A:S.28, A:F.70, A:F.70, A:F.70, A:Y.73, A:Y.73, A:F.77, A:F.77, A:I.81, A:L.84, A:V.118, A:F.120, A:W.133, A:T.156, A:V.160, A:F.171, A:F.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wun, K.S. et al., A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells. Immunity (2011)

Release Date

2011-03-30

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
NKT Valpha14-Jalpha18,NKT Valpha14-Jalpha18: C
Vbeta8.2,Vbeta8.2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

NKT Valpha14-Jalpha18,NKT Valpha14-Jalpha18

Vbeta8.2,Vbeta8.2

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