SMTL ID : 5tw2.1

Structure of mouse CD1d with bound alpha-galactosylsphingamide JG168

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 9 residues within 4Å: Chain A: E.113, S.114, F.128, W.129, G.130, T.131, Q.161, L.164, N.165 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.128, A:L.164 Hydrogen bonds: A:S.114, A:S.114, A:G.130

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

NAG.2: 3 residues within 4Å: Chain A: W.23, S.24, N.42 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:R.74

1 x 7LP: (5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide(Non-covalent)

7LP.3: 18 residues within 4Å: Chain A: Y.73, S.76, F.77, D.80, I.81, L.84, I.98, V.118, F.120, W.133, L.143, L.150, D.153, G.155, T.156, V.160, L.163 Ligands: PLM.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.73, A:F.77, A:I.81, A:L.84, A:I.98, A:V.118, A:F.120, A:W.133, A:L.143, A:T.156, A:V.160, A:L.163 Hydrogen bonds: A:G.155, A:T.156, A:T.156, A:T.156 Water bridges: A:Y.73

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.4: 13 residues within 4Å: Chain A: F.10, Q.14, S.28, V.30, W.40, W.63, L.66, F.70, A.102, L.163, C.168, F.171 Ligands: 7LP.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.10, A:W.40, A:W.63, A:L.66, A:A.102, A:F.171 Hydrogen bonds: A:Q.14, A:S.28

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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