SMTL ID : 3u0p.3 (2 other biounits)

Crystal structure of human CD1d-lysophosphatidylcholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 4 residues within 4Å: Chain A: N.21, S.23, W.24 Chain B: D.37 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.37, A:W.24, A:N.21

1 x NBU: N-BUTANE(Non-covalent)

NBU.2: 4 residues within 4Å: Chain A: D.81, L.149, D.152, T.155 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.149, A:D.152

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain B: S.60, K.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Sagaseta, J. et al., Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor. Embo J. (2012)

Release Date

2012-04-25

Peptides

Antigen-presenting glycoprotein CD1d: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Antigen-presenting glycoprotein CD1d

Beta-2-microglobulin

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