SMTL ID : 5tw5.1

Structure of mouse CD1d with bound glycosphingolipid JJ112

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 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)

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.2: 14 residues within 4Å: Chain A: F.10, Q.14, S.28, V.30, W.40, I.47, W.63, L.66, F.70, Y.73, A.102, L.163, L.164, F.171 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.10, A:V.30, A:W.40, A:I.47, A:W.63, A:L.66, A:F.70, A:A.102, A:L.164, A:F.171 Hydrogen bonds: A:S.28

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: 3 residues within 4Å: Chain A: W.23, S.24, N.42 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:S.24, A:S.24, A:R.74

1 x 7LM: N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxy-16-phenylhexadecan-2-yl]octanamide(Non-covalent)

7LM.5: 18 residues within 4Å: Chain A: V.72, Y.73, S.76, F.77, D.80, L.84, I.98, V.118, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, T.159, V.160 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.73, A:Y.73, A:Y.73, A:F.77, A:F.77, A:I.98, A:V.118, A:F.120, A:W.133, A:L.143, A:T.156, A:T.159, A:V.160 Hydrogen bonds: A:D.153, A:G.155, A:T.156, A:T.156, A:T.156 Water bridges: A:Y.73, A:D.153, A:T.156 pi-Stacking: A:W.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guillaume, J. et al., Galactosylsphingamides: new alpha-GalCer analogues to probe the F'-pocket of CD1d. Sci Rep (2017)

Release Date

2017-09-20

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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