SMTL ID : 2fik.1

Structure of a microbial glycosphingolipid bound to mouse CD1d

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:R.25, A:N.42 Water bridges: A:S.24, A:S.24, A:T.26 NAG.3: 3 residues within 4Å: Chain A: A.19, N.20, W.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20

1 x GSL: (2S,3R)-3-HYDROXY-2-(TETRADECANOYLAMINO)OCTADECYL ALPHA-D-GALACTOPYRANOSIDURONIC ACID(Non-covalent)

GSL.4: 26 residues within 4Å: Chain A: C.12, Q.14, S.28, F.70, V.72, Y.73, S.76, F.77, D.80, I.81, L.84, I.96, L.100, L.116, V.118, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, T.159, V.160 Ligands: PLM.5 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.70, A:Y.73, A:Y.73, A:F.77, A:I.81, A:L.84, A:I.96, A:L.100, A:L.116, A:F.120, A:F.120, A:W.133, A:L.143, A:L.150, A:T.159, A:V.160 Hydrogen bonds: A:D.80, A:T.156, A:T.156 Water bridges: A:S.76, A:R.79, A:R.79

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 17 residues within 4Å: Chain A: F.10, S.28, V.30, W.40, I.47, W.63, L.66, F.70, A.102, L.116, V.160, L.163, L.164, T.167, C.168, F.171 Ligands: GSL.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.10, A:V.30, A:I.47, A:W.63, A:L.66, A:F.70, A:F.70, A:A.102, A:L.116, A:V.160, A:L.163, A:T.167, A:F.171, A:F.171 Hydrogen bonds: A:S.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, D. et al., Design of natural killer T cell activators: structure and function of a microbial glycosphingolipid bound to mouse CD1d. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-03-21

Peptides

T-cell surface glycoprotein CD1d1: A
B(2)-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

T-cell surface glycoprotein CD1d1

B(2)-microglobulin

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