SMTL ID : 1z5l.3 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

2 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 NAG-NAG.6: 5 residues within 4Å: Chain C: W.129, G.130, T.131, Q.161, N.165 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.131

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

NAG.2: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20 NAG.3: 3 residues within 4Å: Chain A: W.23, S.24, N.42 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24 Water bridges: A:N.42, A:R.74 NAG.7: 3 residues within 4Å: Chain C: W.23, S.24, N.42 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.23 Hydrogen bonds: C:S.24, C:N.42 Water bridges: C:D.43, C:R.74

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

PBS.4: 18 residues within 4Å: Chain A: Y.73, S.76, F.77, R.79, D.80, I.81, L.84, V.85, L.116, W.133, W.142, L.143, L.150, D.153, G.155, T.156, V.160 Ligands: R16.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.73, A:F.77, A:I.81, A:L.84, A:V.85, A:L.116, A:W.133, A:W.133, A:W.142, A:L.143, A:L.150, A:V.160 Hydrogen bonds: A:R.79, A:D.80, A:D.80, A:G.155, A:T.156, A:T.156 PBS.8: 17 residues within 4Å: Chain C: 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 C Hydrophobic interactions: C:Y.73, C:Y.73, C:F.77, C:F.77, C:L.84, C:V.85, C:V.118, C:W.133, C:W.133, C:W.142, C:L.143, C:T.156, C:V.160, C:L.163 Hydrogen bonds: C:R.79, C:D.80, C:G.155, C:T.156, C:T.156, C:T.156

2 x R16: HEXADECANE(Non-covalent)

R16.5: 10 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, W.63, F.70, C.168, F.171 Ligands: PBS.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.10, A:Q.14, A:V.30, A:W.63, A:F.70, A:F.70, A:F.171 R16.9: 9 residues within 4Å: Chain C: 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 C Hydrophobic interactions: C:F.10, C:Q.14, C:L.66, C:F.70, C:F.70, C:F.70, C:A.102, C:F.171, C: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: AC
Beta-2-microglobulin: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

T-cell surface glycoprotein CD1d antigen

Beta-2-microglobulin

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