SMTL ID : 4wwk.1

Crystal structure of human TCR Alpha Chain-TRAV12-3, Beta Chain-TRBV6-5, Antigen-presenting molecule CD1d, and Beta-2-microglobulin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain C: A.20, N.21, S.23, W.24 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.23, C:S.23 NAG.2: 4 residues within 4Å: Chain C: W.24, T.25, R.26, N.43 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.24 Hydrogen bonds: C:T.25, C:R.26, C:N.43

1 x JLS: (15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide(Non-covalent)

JLS.3: 31 residues within 4Å: Chain B: Q.100 Chain C: C.13, L.14, Q.15, L.30, A.31, W.41, V.48, I.70, F.71, V.73, Y.74, S.77, F.78, D.81, V.82, F.85, L.91, L.95, F.115, F.119, W.132, W.141, L.149, D.152, W.154, T.155, T.158, V.159, L.162, F.170 36 PLIP interactions: 35 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Q.15, C:A.31, C:W.41, C:W.41, C:V.48, C:I.70, C:F.71, C:F.71, C:F.71, C:F.71, C:Y.74, C:Y.74, C:Y.74, C:F.78, C:V.82, C:F.85, C:F.85, C:L.91, C:L.95, C:F.115, C:F.119, C:W.132, C:W.141, C:L.149, C:T.155, C:T.158, C:V.159, C:L.162, C:F.170, C:F.170 Hydrogen bonds: C:S.77, C:D.152, C:D.152, C:T.155, C:T.155, B:Q.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Le Nours, J. et al., Atypical natural killer T-cell receptor recognition of CD1d-lipid antigens. Nat Commun (2016)

Release Date

2016-02-03

Peptides

TCR Alpha Chain-TRAV12-3: A
TCR Beta Chain-TRBV6-5: B
Antigen-presenting glycoprotein CD1d: C
Beta-2-microglobulin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

TCR Alpha Chain-TRAV12-3

TCR Beta Chain-TRBV6-5

Antigen-presenting glycoprotein CD1d

Beta-2-microglobulin

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