SMTL ID : 3g08.1

Crystal structure of the alpha-galactosylceramide analog OCH in complex with mouse CD1d

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 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)

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

NAG.2: 3 residues within 4Å: Chain A: A.19, N.20, W.23 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.20, A:N.20 NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.23, A:R.25 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:R.74

1 x FEE: N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyoctyl}tetracosanamide(Non-covalent)

FEE.4: 25 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, W.40, I.47, W.63, M.69, F.70, V.72, Y.73, S.76, D.80, L.116, W.133, L.150, D.153, G.155, T.156, T.159, V.160, L.163, C.168, F.171 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.10, A:Q.14, A:V.30, A:W.40, A:I.47, A:W.63, A:F.70, A:Y.73, A:Y.73, A:L.116, A:W.133, A:W.133, A:T.159, A:V.160, A:F.171, A:F.171 Hydrogen bonds: A:D.80, A:D.80, A:G.155, A:T.156, A:T.156 Water bridges: A:D.153

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 3 residues within 4Å: Chain A: D.80, V.118, L.143 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.118, A:L.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sullivan, B.A. et al., Mechanisms for glycolipid antigen-driven cytokine polarization by Valpha14i NKT cells. J.Immunol. (2010)

Release Date

2009-12-08

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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