SMTL ID : 4mq7.1

Structure of human CD1d-sulfatide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: W.24, T.25, R.26, N.43 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.26 Hydrogen bonds: A:T.25 Water bridges: A:T.27

1 x CIS: (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE(Non-covalent)

CIS.2: 31 residues within 4Å: Chain A: L.11, C.13, L.14, Q.15, L.30, H.39, W.41, V.48, W.64, L.67, F.71, Y.74, S.77, F.78, D.81, V.82, F.85, L.91, L.97, F.115, V.117, F.119, L.125, W.132, L.149, D.152, W.154, T.155, T.158, L.162, F.170 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:L.11, A:Q.15, A:H.39, A:V.48, A:W.64, A:L.67, A:F.71, A:F.71, A:Y.74, A:Y.74, A:Y.74, A:F.78, A:V.82, A:F.85, A:F.85, A:L.91, A:L.97, A:F.115, A:V.117, A:V.117, A:F.119, A:L.125, A:W.132, A:W.132, A:L.149, A:W.154, A:T.155, A:T.158, A:F.170 Hydrogen bonds: A:D.81, A:T.155, A:T.155, A:T.155, A:T.155 Water bridges: A:Y.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luoma, A.M. et al., Crystal Structure of V delta 1 T Cell Receptor in Complex with CD1d-Sulfatide Shows MHC-like Recognition of a Self-Lipid by Human gamma delta T Cells. Immunity (2013)

Release Date

2013-12-18

Peptides

Antigen-presenting glycoprotein CD1d, Cd1d1 protein: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Antigen-presenting glycoprotein CD1d, Cd1d1 protein

Beta-2-microglobulin

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