SMTL ID : 3tn0.1

Structure of mouse Va14Vb8.2NKT TCR-mouse CD1d-a-C-Galactosylceramide complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 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.129, G.130, Q.161, N.165 No protein-ligand interaction detected (PLIP)

1 x QUX: N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide(Non-covalent)

QUX.2: 28 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, I.47, W.63, M.69, F.70, Y.73, S.76, F.77, D.80, L.100, F.120, W.133, L.150, D.153, G.155, T.156, V.160, L.163, L.164, C.168 Chain C: P.28, N.30, D.93, R.94, G.95 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:V.30, A:I.47, A:W.63, A:F.70, A:Y.73, A:Y.73, A:F.77, A:L.100, A:F.120, A:W.133, A:L.150, A:T.156, A:V.160, A:L.163, A:L.164 Hydrogen bonds: A:D.80, A:D.153, A:T.156, A:T.156, C:N.30, C:R.94, C:G.95

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patel, O. et al., NKT TCR Recognition of CD1d-{alpha}-C-Galactosylceramide. J.Immunol. (2011)

Release Date

2011-12-14

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2 microglobulin: B
mouse NKT Valpha14 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN): C
mouse NKT Vbeta8.2 (MOUSE VARIABLE DOMAIN, 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

mouse NKT Valpha14 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)

mouse NKT Vbeta8.2 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)

Related Entries With Identical Sequence