SMTL ID : 4f7e.1

Crystal structure of bovine CD1d with bound C16:0-alpha-galactosyl ceramide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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: N.20, S.22, W.23 No protein-ligand interaction detected (PLIP)

1 x 0SH: N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexadecanamide(Non-covalent)

0SH.2: 20 residues within 4Å: Chain A: Q.14, A.30, L.70, Y.73, S.76, F.77, R.79, D.80, I.81, F.84, L.94, I.96, I.98, T.100, L.124, W.131, T.154, T.157, V.158, L.161 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Q.14, A:A.30, A:L.70, A:Y.73, A:Y.73, A:Y.73, A:I.81, A:F.84, A:L.94, A:I.96, A:I.96, A:I.98, A:L.124, A:L.124, A:W.131, A:T.157, A:V.158, A:L.161 Hydrogen bonds: A:S.76, A:S.76, A:R.79, A:R.79, A:D.80, A:D.80, A:N.151, A:T.154

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

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

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

SO4.4: 5 residues within 4Å: Chain B: P.5, K.6, I.7, Q.8, R.90 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.7, B:I.7, B:Q.8 Salt bridges: B:R.90

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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