SMTL ID : 6cyw.1

Structure of sphingomyelin in complex with mouse CD1d

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 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: 4 residues within 4Å: Chain A: 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: 3 residues within 4Å: Chain A: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, N.42, D.43 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:S.24, A:S.24

1 x FO4: sphingomyelin(Non-covalent)

FO4.4: 29 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, I.47, L.66, F.70, Y.73, S.76, F.77, R.79, D.80, I.81, L.84, I.98, L.100, V.118, F.120, W.133, W.142, L.143, L.150, G.155, T.156, T.159, V.160, L.163, F.171 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.10, A:V.30, A:I.47, A:L.66, A:Y.73, A:Y.73, A:Y.73, A:I.81, A:L.84, A:L.100, A:V.118, A:F.120, A:W.133, A:W.142, A:L.150, A:L.150, A:V.160, A:L.163, A:F.171 Hydrogen bonds: A:S.76, A:R.79, A:T.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Melum, E. et al., Control of CD1d-restricted antigen presentation and inflammation by sphingomyelin. Nat.Immunol. (2019)

Release Date

2019-04-10

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

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