SMTL ID : 6ojp.1

Structure of glycolipid alpha-GSA[8,6P] in complex with mouse CD1d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 8 residues within 4Å: Chain A: E.113, S.114, W.129, G.130, T.131, Q.161, L.164, N.165 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.164, A:W.129 Hydrogen bonds: A:S.114, A:S.114, A:G.130

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

NAG-NAG-BMA-MAN-MAN.2: 14 residues within 4Å: Chain A: N.7, Y.8, T.9, G.33, K.216, R.234, G.235, D.236, F.237 Chain B: Y.26, T.28, Q.29, S.57, Y.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.236, A:F.237, A:R.234, A:R.234, A:K.216, A:K.216

2 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 No protein-ligand interaction detected (PLIP) NAG.4: 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:R.25, A:N.42

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.5: 17 residues within 4Å: Chain A: H.73, S.76, F.77, D.80, I.81, L.84, I.98, V.118, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, V.160 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:H.73, A:I.81, A:L.84, A:I.98, A:V.118, A:F.120, A:L.143, A:L.150, A:T.156, A:V.160 Hydrogen bonds: A:G.155, A:T.156, A:T.156, A:T.156 pi-Stacking: A:W.142

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.6: 16 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, W.40, I.47, W.63, L.66, F.70, H.73, R.74, A.102, L.163, C.168, F.171 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.10, A:V.30, A:I.47, A:W.63, A:L.66, A:F.70, A:F.70, A:A.102, A:L.163, A:F.171, A:F.171 Hydrogen bonds: A:S.28, A:R.74 Water bridges: A:H.73 Salt bridges: A:H.73

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 10 residues within 4Å: Chain A: W.192, S.194, H.209, Y.246 Chain B: V.9, Y.10, S.11, P.15, W.95, D.96 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.11, B:W.95, A:S.194, A:S.194, A:Y.246, A:Y.246 Water bridges: B:D.96 GOL.9: 8 residues within 4Å: Chain A: W.31, P.239, N.240 Chain B: S.52, D.53, Y.63, L.65 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.52 GOL.10: 3 residues within 4Å: Chain A: H.117, Y.124 Chain B: W.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.60 GOL.11: 8 residues within 4Å: Chain B: D.76, T.77, Y.78, W.95, D.96, R.97, D.98, M.99 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.78, B:Y.78, B:D.96, B:D.98, B:M.99

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 7 residues within 4Å: Chain A: D.34, P.239, N.240, E.243, T.244, W.245 Ligands: GOL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.34, A:T.244 Water bridges: A:E.243

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

2019-08-21

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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