SMTL ID : 3au1.1

Crystal structure of mouse CD1d in complex with ganglioside GD3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- GLC- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-GLC-MAN-MAN.1: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- GLC- MAN- BMA- FUC: alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-glucopyranose-(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-GLC-MAN-BMA-FUC.2: 9 residues within 4Å: Chain A: E.113, S.114, F.128, W.129, G.130, T.131, Q.161, L.164, N.165 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.128, A:L.164 Hydrogen bonds: A:E.113, A:S.114, A:S.114, A:G.130

1 x BGC- GAL: beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GAL.3: 3 residues within 4Å: Chain A: D.153, T.156 Ligands: ERA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.153, A:D.153

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

NAG.4: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 No protein-ligand interaction detected (PLIP)

1 x ERA: (7Z,15E,17E)-N-[(2S,3S,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tricosa-7,15,17-trienamide(Non-covalent)

ERA.5: 18 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, I.47, F.70, Y.73, S.76, D.80, I.98, L.100, A.102, V.118, W.133, T.156, T.159, V.160 Ligands: BGC-GAL.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.30, A:I.47, A:F.70, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:I.98, A:L.100, A:A.102, A:V.118, A:W.133, A:T.156, A:T.159, A:V.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mallevaey, T. et al., A molecular basis for NKT cell recognition of CD1d-self-antigen. Immunity (2011)

Release Date

2011-10-12

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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