SMTL ID : 5w3s.1

Cryo-electron microscopy structure of a TRPML3 ion channel

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 14 residues within 4Å: Chain A: C.416, A.419, A.420, Y.423, L.424, L.444, N.445, S.448, I.455, F.497 Chain B: Y.491 Chain C: L.82 Ligands: Y01.7, 3PE.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.419, A:I.455 Y01.5: 11 residues within 4Å: Chain A: C.50, I.67, I.70, A.71, T.74, I.75, W.385, V.388, Y.391, F.394, F.395 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.67, A:I.67, A:I.70, A:A.71, A:T.74, A:I.75, A:W.385, A:V.388, A:Y.391 Y01.6: 11 residues within 4Å: Chain A: Y.472, W.475, L.476, R.479, I.480, Y.483, S.484, S.487 Chain C: C.416, N.445 Ligands: Y01.16 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.472, A:W.475, A:I.480, A:I.480, A:Y.483 Hydrogen bonds: C:N.445 Y01.7: 12 residues within 4Å: Chain A: C.416, N.445 Chain B: Y.472, W.475, L.476, R.479, I.480, Y.483, S.484, S.487, Y.491 Ligands: Y01.1 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.472, B:W.475, B:I.480, B:I.480, B:Y.483 Hydrogen bonds: A:N.445 Y01.8: 15 residues within 4Å: Chain A: L.82 Chain B: C.416, A.419, A.420, Y.423, L.424, C.427, L.444, N.445, S.448, I.455, F.497 Chain D: Y.491 Ligands: 3PE.4, Y01.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.419, B:I.455 Y01.10: 11 residues within 4Å: Chain B: C.50, I.67, I.70, A.71, T.74, I.75, W.385, V.388, Y.391, F.394, F.395 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.67, B:I.67, B:I.70, B:A.71, B:T.74, B:I.75, B:W.385, B:V.388, B:Y.391 Y01.12: 11 residues within 4Å: Chain C: C.50, I.67, I.70, A.71, T.74, I.75, W.385, V.388, Y.391, F.394, F.395 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.67, C:I.67, C:I.70, C:A.71, C:T.74, C:W.385, C:V.388, C:Y.391, C:F.395 Y01.16: 15 residues within 4Å: Chain A: Y.491 Chain C: C.416, A.419, A.420, Y.423, L.424, C.427, L.444, N.445, S.448, I.455, F.497 Chain D: L.82 Ligands: Y01.6, 3PE.20 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.419, C:Y.423, C:I.455 Y01.17: 11 residues within 4Å: Chain C: Y.472, W.475, L.476, R.479, I.480, Y.483, S.484, S.487 Chain D: C.416, N.445 Ligands: Y01.22 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.472, C:W.475, C:L.476, C:I.480, C:I.480, C:Y.483, C:Y.483 Hydrogen bonds: D:N.445 Y01.19: 11 residues within 4Å: Chain B: C.416, N.445 Chain D: Y.472, W.475, L.476, R.479, I.480, Y.483, S.484, S.487 Ligands: Y01.8 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.472, D:W.475, D:L.476, D:R.479, D:I.480, D:I.480, D:Y.483 Hydrogen bonds: B:N.445 Y01.21: 11 residues within 4Å: Chain D: C.50, I.67, I.70, A.71, T.74, I.75, W.385, V.388, Y.391, F.394, F.395 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.67, D:I.67, D:I.70, D:A.71, D:T.74, D:W.385, D:V.388, D:Y.391 Y01.22: 15 residues within 4Å: Chain B: L.82 Chain C: Y.483, Y.491 Chain D: C.416, A.419, A.420, Y.423, L.424, L.444, N.445, S.448, I.455, F.497 Ligands: 3PE.9, Y01.17 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.419, D:A.420, D:I.455

6 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: G.457 Chain B: G.457 Chain C: G.457 Chain D: G.457 Ligands: NA.13, NA.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.456 NA.3: 4 residues within 4Å: Chain A: I.498 Chain B: I.498 Chain C: I.498 Chain D: I.498 No protein-ligand interaction detected (PLIP) NA.13: 7 residues within 4Å: Chain A: D.458 Chain B: D.458 Chain C: G.457, D.458 Chain D: G.457, D.458 Ligands: NA.2 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.457 NA.14: 2 residues within 4Å: Ligands: NA.2, NA.15 No protein-ligand interaction detected (PLIP) NA.15: 1 residues within 4Å: Ligands: NA.14 No protein-ligand interaction detected (PLIP) NA.18: 4 residues within 4Å: Chain A: D.458 Chain B: D.458 Chain C: D.458 Chain D: D.458 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.458

4 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.4: 8 residues within 4Å: Chain A: V.78, W.385, L.392, F.395, Y.398 Chain B: L.424, F.428 Ligands: Y01.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.395 3PE.9: 8 residues within 4Å: Chain B: V.78, W.385, L.392, F.395, Y.398 Chain D: L.424, F.428 Ligands: Y01.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.395 3PE.11: 8 residues within 4Å: Chain A: L.424, F.428 Chain C: V.78, W.385, L.392, F.395, Y.398 Ligands: Y01.1 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.395 3PE.20: 8 residues within 4Å: Chain C: L.424, F.428 Chain D: V.78, W.385, L.392, F.395, Y.398 Ligands: Y01.16 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.395

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirschi, M. et al., Cryo-electron microscopy structure of the lysosomal calcium-permeable channel TRPML3. Nature (2017)

Release Date

2017-10-11

Peptides

Mucolipin-3 isoform 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Mucolipin-3 isoform 1