SMTL ID : 3u0p.1 (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- NAG- FUC: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG-FUC.1: 4 residues within 4Å: Chain A: A.20, N.21, S.23, W.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.21

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: 13 residues within 4Å: Chain A: V.73, Y.74, S.77, F.78, R.80, D.81, F.85, L.91, F.119, W.132, W.141, W.154, T.155 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.74, A:F.85, A:L.91, A:F.119, A:W.132, A:W.132, A:W.141 Hydrogen bonds: A:S.77 Salt bridges: A:R.80 pi-Cation interactions: A:W.154, A:W.154

1 x HEX: HEXANE(Non-covalent)

HEX.3: 3 residues within 4Å: Chain A: L.67, C.167 Ligands: UND.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.67

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

SO4.4: 2 residues within 4Å: Chain A: K.153, R.156 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.153, A:K.153, A:R.156 Salt bridges: A:K.153, A:R.156 SO4.5: 3 residues within 4Å: Chain A: F.114, H.116, Q.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.128 Water bridges: A:H.116, A:S.126, A:S.126 Salt bridges: A:H.116 SO4.6: 3 residues within 4Å: Chain A: L.91, S.92, Y.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.93

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: E.181, K.184, Y.213, D.241, E.242, T.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.181, A:K.184, A:E.242, A:E.242 GOL.8: 5 residues within 4Å: Chain A: G.234, D.235, L.246, R.247 Chain B: Q.11 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.235, A:R.247, A:R.247, B:Q.11 Water bridges: B:V.12 GOL.10: 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, B:Y.81 GOL.11: 3 residues within 4Å: Chain B: S.60, K.61, D.62 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.61, B:D.62, B:D.62

1 x UND: UNDECANE(Non-covalent)

UND.9: 11 residues within 4Å: Chain A: C.13, L.14, Q.15, L.30, A.31, H.39, W.41, F.71, Y.74, F.170 Ligands: HEX.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.15, A:A.31, A:W.41, A:F.71, A:F.170

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
A

B
B

Antigen-presenting glycoprotein CD1d

Beta-2-microglobulin

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