SMTL ID : 6c5m.1

Structure of glycolipid aGSA[8,9] in complex with mouse CD1d

Coordinates

PDB Format

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: 3 residues within 4Å: Chain A: W.23, S.24, N.42 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.2: 8 residues within 4Å: Chain A: E.113, S.114, W.129, G.130, T.131, Q.161, L.164, N.165 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: 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.3: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.22

1 x J81: (5R,6S,7S)-5,6-dihydroxy-N-nonyl-7-(octanoylamino)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide (non-preferred name)(Non-covalent)

J81.4: 17 residues within 4Å: Chain A: Y.73, S.76, F.77, R.79, D.80, I.98, V.118, F.120, V.126, W.133, W.142, L.143, L.150, D.153, G.155, T.156, V.160 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.73, A:Y.73, A:Y.73, A:I.98, A:V.118, A:F.120, A:V.126, A:W.142, A:L.150, A:T.156, A:V.160 Hydrogen bonds: A:R.79, A:D.80, A:G.155, A:T.156, A:T.156

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 14 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, W.40, I.47, L.66, F.70, Y.73, A.102, L.163, C.168, F.171 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.10, A:W.40, A:I.47, A:L.66, A:A.102, A:F.171 Hydrogen bonds: A:S.28

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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