SMTL ID : 6c6a.1

Structure of glycolipid aGSA[16,6P] in complex with mouse CD1d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-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 No protein-ligand interaction detected (PLIP)

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: 3 residues within 4Å: Chain A: W.23, S.24, 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 EL7: N-[(2S,3S,4R)-3,4-dihydroxy-8-oxo-8-[(6-phenylhexyl)amino]-1-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octan-2-yl]heptadecanamide (non-preferred name)(Non-covalent)

EL7.4: 19 residues within 4Å: Chain A: Q.14, S.28, F.70, Y.73, S.76, F.77, D.80, I.81, L.84, L.100, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, V.160 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.70, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:F.77, A:I.81, A:L.84, A:L.100, A:F.120, A:W.142, A:L.143, A:L.150, A:L.150, A:T.156, A:V.160 Hydrogen bonds: A:S.76, A:S.76, A:T.156, A:T.156 Water bridges: A:D.153, A:T.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., A molecular switch in mouse CD1d modulates natural killer T cell activation by alpha-galactosylsphingamides. J.Biol.Chem. (2019)

Release Date

2019-01-30

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

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