SMTL ID : 3ilp.1

Structure of mCD1d with bound glycolipid BbGL-2f from Borrelia burgdorferi

Coordinates

PDB Format Compare

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

NAG.2: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.23, A:R.25 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:S.24, A:S.24

1 x 1L2: (2S)-3-(alpha-D-galactopyranosyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl (9Z,12Z)-octadeca-9,12-dienoate(Non-covalent)

1L2.3: 31 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, I.47, W.63, M.69, F.70, V.72, Y.73, S.76, F.77, R.79, D.80, L.84, I.96, I.98, V.118, F.120, W.133, W.142, L.143, I.147, D.153, G.155, T.156, T.159, V.160, F.171 Ligands: DMS.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.10, A:V.30, A:I.47, A:W.63, A:F.70, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:F.77, A:I.96, A:I.98, A:V.118, A:W.133, A:L.143, A:I.147, A:V.160, A:F.171 Hydrogen bonds: A:S.76, A:S.76, A:R.79, A:T.156, A:T.156 Water bridges: A:D.153

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 6 residues within 4Å: Chain A: D.80, I.81, L.84, P.146, I.147 Ligands: 1L2.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Lipid binding orientation within CD1d affects recognition of Borrelia burgorferi antigens by NKT cells. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-01-26

Peptides

T-cell surface glycoprotein CD1d1: A
Beta-2 microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

T-cell surface glycoprotein CD1d1

Beta-2 microglobulin

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