SMTL ID : 8wr3.1

Cryo-EM structure of lysosomal protein LYCHOS

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 11 residues within 4Å: Chain A: F.276, I.280, I.283, T.284, L.288, I.349, V.353, I.357, L.660, I.710 Ligands: POV.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.276, A:F.276, A:I.283, A:L.288, A:I.349, A:I.349, A:V.353, A:L.660, A:I.710 CLR.6: 11 residues within 4Å: Chain B: F.276, I.280, I.283, T.284, L.288, I.349, V.353, I.357, L.660, I.710 Ligands: POV.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.276, B:F.276, B:I.283, B:L.288, B:I.349, B:I.349, B:V.353, B:V.353, B:I.357, B:L.660, B:I.710

6 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.2: 31 residues within 4Å: Chain A: F.43, L.46, L.47, F.50, V.53, L.54, Y.57, R.61, M.264, V.265, G.266, K.267, I.268, R.270, V.348, F.352, V.353, A.355, P.356, Y.359, V.360, I.386, V.389, R.657, F.695, F.705, I.706, L.713, D.714 Ligands: CLR.1, POV.5 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:F.43, A:L.46, A:L.47, A:F.50, A:V.53, A:L.54, A:Y.57, A:F.352, A:F.352, A:F.352, A:F.352, A:V.353, A:P.356, A:Y.359, A:V.360, A:I.386, A:V.389, A:F.695, A:F.705, A:I.706, A:L.713 Hydrogen bonds: A:Y.57, A:R.61, A:G.266, A:K.267, A:I.268 Salt bridges: A:D.714 POV.3: 12 residues within 4Å: Chain A: L.120, T.121, V.124, A.125, S.126, K.133, V.277, V.278, L.281, L.282, T.284, A.285 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.120, A:T.121, A:V.124, A:A.125, A:V.277, A:L.281, A:L.281, A:L.282, A:T.284, A:A.285 Hydrogen bonds: A:S.126, A:S.126 POV.5: 14 residues within 4Å: Chain A: L.47, L.54, I.58, R.61, A.62, N.63, I.388, V.389, I.392, W.396, F.708, L.713, K.715 Ligands: POV.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.54, A:I.58, A:I.58, A:I.58, A:I.388, A:V.389, A:I.392, A:W.396, A:W.396, A:W.396, A:F.708, A:F.708, A:L.713 Salt bridges: A:R.61, A:R.61, A:K.715 POV.7: 27 residues within 4Å: Chain B: F.43, L.46, L.47, F.50, V.53, Y.57, R.61, M.264, V.265, G.266, K.267, I.268, R.270, F.352, V.353, A.355, P.356, Y.359, V.360, V.389, R.657, F.695, I.706, L.713, D.714 Ligands: CLR.6, POV.10 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:F.43, B:L.46, B:L.46, B:L.47, B:F.50, B:F.50, B:V.53, B:Y.57, B:F.352, B:F.352, B:F.352, B:V.353, B:P.356, B:P.356, B:Y.359, B:V.360, B:V.389, B:F.695, B:I.706, B:L.713 Hydrogen bonds: B:Y.57, B:R.61, B:G.266, B:K.267, B:I.268 Salt bridges: B:D.714 POV.8: 12 residues within 4Å: Chain B: L.120, T.121, V.124, A.125, S.126, K.133, V.277, V.278, L.281, L.282, T.284, A.285 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.120, B:T.121, B:V.124, B:A.125, B:V.277, B:L.281, B:L.281, B:L.282, B:T.284, B:A.285 Hydrogen bonds: B:S.126, B:S.126 POV.10: 16 residues within 4Å: Chain B: L.47, L.54, I.58, R.61, A.62, N.63, I.388, V.389, I.392, S.393, W.396, F.708, L.713, K.715, H.716 Ligands: POV.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.58, B:I.58, B:I.58, B:I.388, B:V.389, B:I.392, B:W.396, B:W.396, B:W.396, B:F.708, B:L.713 Salt bridges: B:R.61, B:R.61, B:K.715

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

NAG.4: 3 residues within 4Å: Chain A: Y.162, S.306, N.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.306 NAG.9: 3 residues within 4Å: Chain B: Y.162, S.306, N.309 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.306, B:N.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z.H. et al., Structural and biochemical verification of LYCHOS as a tryptophan transporter. To Be Published

Release Date

2025-01-15

Peptides

Lysosomal cholesterol signaling protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Lysosomal cholesterol signaling protein