SMTL ID : 1z5l.2 (2 other biounits)

Structure of a highly potent short-chain galactosyl ceramide agonist bound to CD1D

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.131

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

NAG.2: 3 residues within 4Å: Chain A: W.23, S.24, N.42 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:D.43, A:R.74

1 x PBS: (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL(Non-covalent)

PBS.3: 17 residues within 4Å: Chain A: Y.73, S.76, F.77, R.79, D.80, L.84, V.85, V.118, W.133, W.142, L.143, L.150, D.153, G.155, T.156, V.160, L.163 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.73, A:Y.73, A:F.77, A:F.77, A:L.84, A:V.85, A:V.118, A:W.133, A:W.133, A:W.142, A:L.143, A:T.156, A:V.160, A:L.163 Hydrogen bonds: A:R.79, A:D.80, A:D.80, A:G.155, A:T.156, A:T.156

1 x R16: HEXADECANE(Non-covalent)

R16.4: 9 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, L.66, F.70, A.102, C.168, F.171 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.10, A:Q.14, A:L.66, A:F.70, A:F.70, A:F.70, A:A.102, A:F.171, A:F.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zajonc, D.M. et al., Structure and function of a potent agonist for the semi-invariant natural killer T cell receptor. Nat.Immunol. (2005)

Release Date

2005-07-19

Peptides

T-cell surface glycoprotein CD1d antigen: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

T-cell surface glycoprotein CD1d antigen

Beta-2-microglobulin

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