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

Crystal structure of human CD1d-lysophosphatidylcholine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC- FUC: alpha-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-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 Hydrophobic interactions: A:W.24

1 x LSC: (4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide(Non-covalent)

LSC.2: 12 residues within 4Å: Chain A: Y.74, S.77, F.78, D.81, F.85, L.97, W.132, W.141, D.152, W.154, T.155, V.159 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.74, A:F.78, A:F.85, A:W.132, A:W.141, A:W.154 Hydrogen bonds: A:T.155, A:T.155 pi-Cation interactions: A:W.154

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

SO4.3: 2 residues within 4Å: Chain A: P.200, G.201 No protein-ligand interaction detected (PLIP) SO4.4: 4 residues within 4Å: Chain A: V.217, W.218, V.219, P.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.219 SO4.5: 3 residues within 4Å: Chain A: Q.226, Q.228, Q.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.227, A:Q.229 SO4.7: 2 residues within 4Å: Chain A: R.247 Chain B: Q.11 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.247 SO4.8: 4 residues within 4Å: Chain B: D.37, N.86, H.87, V.88 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.39 SO4.9: 4 residues within 4Å: Chain B: K.44, F.73, T.74, Y.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.74, B:T.74, B:Y.81 Salt bridges: B:K.44 SO4.11: 2 residues within 4Å: Chain B: R.48, R.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.48 Salt bridges: B:R.84

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: R.263, Q.272, D.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.263, A:Q.272, A:D.273 GOL.10: 1 residues within 4Å: Chain B: N.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.20, B:N.20 GOL.12: 2 residues within 4Å: Chain B: S.60, K.61 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.66

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
C

B
D

Antigen-presenting glycoprotein CD1d

Beta-2-microglobulin

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