SMTL ID : 3rug.1 (1 other biounit)

Crystal structure of Valpha10-Vbeta8.1 NKT TCR in complex with CD1d-alphaglucosylceramide (C20:2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 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 DB6: (11E,14E)-N-[(2S,3S,4R)-1-(alpha-D-glucopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide(Non-covalent)

DB6.2: 27 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, F.70, Y.73, S.76, D.80, L.84, I.98, V.118, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, V.160 Chain C: T.28, L.29, N.30, S.51, W.52, S.92, S.93 27 PLIP interactions: 23 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Q.14, A:V.30, A:F.70, A:F.70, A:Y.73, A:Y.73, A:L.84, A:I.98, A:V.118, A:F.120, A:W.133, A:W.142, A:L.143, A:L.150, A:V.160 Hydrogen bonds: A:S.76, A:D.80, A:D.153, A:G.155, A:G.155, A:T.156, A:T.156, C:N.30, C:S.51, C:S.92 Water bridges: A:D.80, C:S.94

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

NAG.3: 3 residues within 4Å: Chain A: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: G.130, T.131, Q.161, N.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.161, A:Q.161, A:N.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uldrich, A.P. et al., A semi-invariant V(alpha)10(+) T cell antigen receptor defines a population of natural killer T cells with distinct glycolipid antigen-recognition properties. Nat.Immunol. (2011)

Release Date

2011-08-03

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
Valpha10(mouse variable domain, human constant domain): C
Vbeta8.1(mouse variable domain, human constant domain): D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

Valpha10(mouse variable domain, human constant domain)

Vbeta8.1(mouse variable domain, human constant domain)

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