SMTL ID : 4f7c.1 (1 other biounit)

Crystal structure of bovine CD1d with bound C12-di-sulfatide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.86 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: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: W.23, T.24, R.25, N.42 No protein-ligand interaction detected (PLIP)

1 x 0SG: N-{(2S,3R,4E)-1-[(3,6-di-O-sulfo-beta-D-galactopyranosyl)oxy]-3-hydroxyoctadec-4-en-2-yl}dodecanamide(Non-covalent)

0SG.3: 16 residues within 4Å: Chain A: Q.14, V.72, Y.73, S.76, F.77, D.80, I.96, T.100, F.118, L.124, F.140, N.151, G.153, T.154, T.157, L.161 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Q.14, A:Y.73, A:Y.73, A:F.77, A:F.77, A:I.96, A:T.100, A:F.118, A:L.124, A:F.140, A:T.157, A:L.161 Hydrogen bonds: A:S.76, A:D.80, A:N.151, A:G.153, A:T.154, A:T.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Crystal Structures of Bovine CD1d Reveal Altered αGalCer Presentation and a Restricted A' Pocket Unable to Bind Long-Chain Glycolipids. Plos One (2012)

Release Date

2012-11-14

Peptides

CD1D antigen, d polypeptide: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CD1D antigen, d polypeptide

Beta-2-microglobulin

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