SMTL ID : 9hl3.1

TRPML1 in complex with compound 1a

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: R.216, V.236, V.277, N.278, T.280, L.307, T.309 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.236, A:T.238 NAG-NAG.2: 7 residues within 4Å: Chain B: R.216, V.236, V.277, N.278, T.280, L.307, T.309 2 PLIP interactions: 2 interactions with chain B Water bridges: B:V.236, B:T.238 NAG-NAG.3: 8 residues within 4Å: Chain C: R.216, V.236, T.238, V.277, N.278, T.280, L.307, T.309 2 PLIP interactions: 2 interactions with chain C Water bridges: C:V.236, C:T.238 NAG-NAG.4: 8 residues within 4Å: Chain D: R.216, V.236, T.238, V.277, N.278, T.280, L.307, T.309 2 PLIP interactions: 2 interactions with chain D Water bridges: D:V.236, D:T.238

4 x D10: DECANE(Non-covalent)

D10.5: 3 residues within 4Å: Chain A: Y.547, S.548 Ligands: 01.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.547, A:Y.547 D10.10: 3 residues within 4Å: Chain B: Y.547, S.548 Ligands: 01.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.547, B:Y.547 D10.15: 3 residues within 4Å: Chain C: Y.547, S.548 Ligands: 01.24 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.547, C:Y.547 D10.20: 3 residues within 4Å: Chain D: Y.547, S.548 Ligands: 01.9 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.547, D:Y.547

4 x D12: DODECANE(Non-covalent)

D12.6: 3 residues within 4Å: Chain A: L.453, F.456, Y.459 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.453, A:F.456, A:Y.459 D12.11: 3 residues within 4Å: Chain B: L.453, F.456, Y.459 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.453, B:F.456, B:Y.459 D12.16: 3 residues within 4Å: Chain C: L.453, F.456, Y.459 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.453, C:F.456, C:Y.459 D12.21: 3 residues within 4Å: Chain D: L.453, F.456, Y.459 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.453, D:F.456, D:Y.459

4 x OCT: N-OCTANE(Non-covalent)

OCT.7: 1 residues within 4Å: Chain A: M.419 No protein-ligand interaction detected (PLIP) OCT.12: 1 residues within 4Å: Chain B: M.419 No protein-ligand interaction detected (PLIP) OCT.17: 1 residues within 4Å: Chain C: M.419 No protein-ligand interaction detected (PLIP) OCT.22: 1 residues within 4Å: Chain D: M.419 No protein-ligand interaction detected (PLIP)

4 x EUJ: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate(Non-covalent)

EUJ.8: 15 residues within 4Å: Chain A: Y.95, K.103, K.107, R.109, K.110, P.111, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403, R.451 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.359 Hydrogen bonds: A:K.103, A:C.112, A:K.113, A:R.366, A:S.367, A:S.367, A:Y.403, A:R.451 Salt bridges: A:K.103, A:K.107, A:R.109, A:K.113, A:K.113, A:R.366, A:R.370 EUJ.13: 15 residues within 4Å: Chain B: Y.95, K.103, K.107, R.109, K.110, P.111, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403, R.451 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.359 Hydrogen bonds: B:K.103, B:C.112, B:K.113, B:R.366, B:R.366, B:S.367, B:S.367, B:Y.403, B:R.451 Salt bridges: B:K.103, B:K.107, B:R.109, B:K.113, B:K.113, B:R.366, B:R.370 EUJ.18: 15 residues within 4Å: Chain C: Y.95, K.103, K.107, R.109, K.110, P.111, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403, R.451 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.359 Hydrogen bonds: C:K.103, C:C.112, C:K.113, C:R.366, C:S.367, C:S.367, C:Y.403, C:R.451 Salt bridges: C:K.103, C:K.107, C:R.109, C:K.113, C:K.113, C:R.366, C:R.370 EUJ.23: 15 residues within 4Å: Chain D: Y.95, K.103, K.107, R.109, K.110, P.111, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403, R.451 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.359 Hydrogen bonds: D:K.103, D:C.112, D:K.113, D:R.366, D:S.367, D:S.367, D:Y.403, D:R.451 Salt bridges: D:K.103, D:K.107, D:R.109, D:K.113, D:K.113, D:R.366, D:R.370

4 x 01: 2-[2-oxidanylidene-2-[(4R)-2,2,4-trimethyl-3,4-dihydroquinolin-1-yl]ethyl]isoindole-1,3-dione

01.9: 15 residues within 4Å: Chain A: C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.553, V.557, L.558, F.561 Chain D: Y.547, S.551, Y.555 Ligands: D10.20 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:Y.547, A:Y.484, A:F.513, A:F.561 pi-Stacking: A:Y.484 01.14: 15 residues within 4Å: Chain A: Y.547, S.551, Y.555 Chain B: C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.553, V.557, L.558, F.561 Ligands: D10.5 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.547, B:Y.484, B:F.513, B:F.561 pi-Stacking: B:Y.484 01.19: 15 residues within 4Å: Chain B: Y.547, S.551, Y.555 Chain C: C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.553, V.557, L.558, F.561 Ligands: D10.10 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.547, B:Y.555, C:Y.484, C:F.513, C:F.561 pi-Stacking: C:Y.484 01.24: 15 residues within 4Å: Chain C: Y.547, S.551, Y.555 Chain D: C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.553, V.557, L.558, F.561 Ligands: D10.15 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.484, D:F.513, D:F.561, C:Y.547 pi-Stacking: D:Y.484

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reeks, J. et al., Enabling High Throughput Electron Cryo-microscopy for Structure-based Design. To Be Published

Release Date

2025-06-04

Peptides

Mucolipin-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-1

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