SMTL ID : 3he7.1

Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta7 NKT TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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: 5 residues within 4Å: Chain A: W.129, G.130, T.131, Q.161, N.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.129

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

NAG.2: 3 residues within 4Å: Chain A: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42

1 x AGH: N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE(Non-covalent)

AGH.4: 29 residues within 4Å: Chain A: C.12, S.28, V.30, W.63, L.66, F.70, V.72, Y.73, S.76, D.80, I.81, L.84, V.118, F.120, W.133, L.143, L.150, D.153, G.155, T.156, T.159, V.160, C.168, F.171 Chain C: P.28, N.30, D.93, R.94, G.95 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:V.30, A:W.63, A:L.66, A:F.70, A:F.70, A:F.70, A:F.70, A:Y.73, A:I.81, A:L.84, A:V.118, A:F.120, A:W.133, A:W.133, A:W.133, A:L.143, A:L.150, A:V.160, A:F.171 Hydrogen bonds: A:G.155, A:T.156, A:T.156, C:N.30, C:R.94, C:G.95 Water bridges: A:D.153, A:T.156 Salt bridges: C:R.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pellicci, D.G. et al., Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors. Immunity (2009)

Release Date

2009-07-28

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
Valpha14(mouse variable domain, human constant domain): C
Vbeta7(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

Valpha14(mouse variable domain, human constant domain)

Vbeta7(mouse variable domain, human constant domain)

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