SMTL ID : 9hl8.1

TRPML1 in complex with compound 8

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 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain B: R.216, V.236, V.277, N.278, T.280, L.307, T.309 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain C: R.216, V.236, V.277, N.278, T.280, L.307, T.309 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain D: R.216, V.236, V.277, N.278, T.280, L.307, T.309 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.5: 13 residues within 4Å: Chain A: Y.95, K.103, K.107, R.109, K.110, P.111, C.112, K.113, L.363, R.366, S.367, R.370, Y.403 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.95, A:C.112, A:K.113, A:R.366, A:R.366, A:S.367, A:S.367, A:Y.403 Salt bridges: A:K.103, A:K.107, A:R.109, A:K.113, A:K.113, A:R.366, A:R.370 EUJ.15: 13 residues within 4Å: Chain B: Y.95, K.103, K.107, R.109, K.110, P.111, C.112, K.113, L.363, R.366, S.367, R.370, Y.403 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Y.95, B:C.112, B:K.113, B:R.366, B:R.366, B:S.367, B:S.367, B:Y.403 Salt bridges: B:K.103, B:K.107, B:R.109, B:K.113, B:K.113, B:R.366, B:R.370 EUJ.24: 13 residues within 4Å: Chain C: Y.95, K.103, K.107, R.109, K.110, P.111, C.112, K.113, L.363, R.366, S.367, R.370, Y.403 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:Y.95, C:C.112, C:K.113, C:R.366, C:R.366, C:S.367, C:S.367, C:Y.403 Salt bridges: C:K.103, C:K.107, C:R.109, C:K.113, C:K.113, C:R.366, C:R.370 EUJ.35: 13 residues within 4Å: Chain D: Y.95, K.103, K.107, R.109, K.110, P.111, C.112, K.113, L.363, R.366, S.367, R.370, Y.403 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Y.95, D:C.112, D:K.113, D:R.366, D:R.366, D:S.367, D:S.367, D:Y.403 Salt bridges: D:K.103, D:K.107, D:R.109, D:K.113, D:K.113, D:R.366, D:R.370

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

OCT.6: 2 residues within 4Å: Chain A: F.456, Y.459 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.456, A:Y.459 OCT.7: 1 residues within 4Å: Chain A: S.415 No protein-ligand interaction detected (PLIP) OCT.10: 2 residues within 4Å: Chain A: L.485, L.505 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.485, A:L.505 OCT.16: 2 residues within 4Å: Chain B: F.456, Y.459 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.456, B:Y.459 OCT.17: 1 residues within 4Å: Chain B: S.415 No protein-ligand interaction detected (PLIP) OCT.20: 1 residues within 4Å: Chain B: L.505 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.505 OCT.25: 2 residues within 4Å: Chain C: F.456, Y.459 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.456, C:Y.459 OCT.26: 1 residues within 4Å: Chain C: S.415 No protein-ligand interaction detected (PLIP) OCT.29: 1 residues within 4Å: Chain C: L.505 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.505 OCT.36: 2 residues within 4Å: Chain D: F.456, Y.459 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.456, D:Y.459 OCT.37: 1 residues within 4Å: Chain D: S.415 No protein-ligand interaction detected (PLIP) OCT.39: 2 residues within 4Å: Chain D: L.485, L.505 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.485, D:L.505

4 x D10: DECANE(Non-covalent)

D10.8: 3 residues within 4Å: Chain A: G.401, W.402 Ligands: D12.33 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.402 D10.18: 3 residues within 4Å: Chain B: G.401, W.402 Ligands: D12.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.402 D10.27: 3 residues within 4Å: Chain C: G.401, W.402 Ligands: D12.22 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.402 D10.38: 3 residues within 4Å: Chain D: G.401, W.402 Ligands: D12.31 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.402

8 x D12: DODECANE(Non-covalent)

D12.9: 4 residues within 4Å: Chain A: M.474, R.475, C.478 Chain B: Y.459 No protein-ligand interaction detected (PLIP) D12.12: 4 residues within 4Å: Chain A: Y.487, F.541, S.548 Ligands: D10.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.487, A:F.541 D12.14: 4 residues within 4Å: Chain A: Y.459 Chain D: M.474, R.475, C.478 No protein-ligand interaction detected (PLIP) D12.19: 4 residues within 4Å: Chain B: M.474, R.475, C.478 Chain C: Y.459 No protein-ligand interaction detected (PLIP) D12.22: 4 residues within 4Å: Chain B: Y.487, F.541, S.548 Ligands: D10.27 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.487, B:F.541 D12.28: 4 residues within 4Å: Chain C: M.474, R.475, C.478 Chain D: Y.459 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:M.474 D12.31: 4 residues within 4Å: Chain C: Y.487, F.541, S.548 Ligands: D10.38 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.487, C:F.541 D12.33: 4 residues within 4Å: Chain D: Y.487, F.541, S.548 Ligands: D10.8 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.487, D:F.541

4 x HEX: HEXANE(Non-covalent)

HEX.11: 4 residues within 4Å: Chain A: S.504, S.506 Chain D: Q.532 Ligands: 01.34 No protein-ligand interaction detected (PLIP) HEX.21: 4 residues within 4Å: Chain A: Q.532 Chain B: S.504, S.506 Ligands: 01.13 No protein-ligand interaction detected (PLIP) HEX.30: 4 residues within 4Å: Chain B: Q.532 Chain C: S.504, S.506 Ligands: 01.23 No protein-ligand interaction detected (PLIP) HEX.40: 4 residues within 4Å: Chain C: Q.532 Chain D: S.504, S.506 Ligands: 01.32 No protein-ligand interaction detected (PLIP)

4 x 01: [2,3-bis(chloranyl)phenyl]-[5-methoxy-2-methyl-3-(2-morpholin-4-ylethyl)indol-1-yl]methanone

01.13: 14 residues within 4Å: Chain A: Q.543, L.544, Y.547, S.548, S.551, Y.555 Chain B: C.477, V.480, A.481, Y.484, S.509, F.513, I.516 Ligands: HEX.21 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.547, A:Y.547 pi-Stacking: A:Y.547 01.23: 14 residues within 4Å: Chain B: Q.543, L.544, Y.547, S.548, S.551, Y.555 Chain C: C.477, V.480, A.481, Y.484, S.509, F.513, I.516 Ligands: HEX.30 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.547, B:Y.547 pi-Stacking: B:Y.547 01.32: 14 residues within 4Å: Chain C: Q.543, L.544, Y.547, S.548, S.551, Y.555 Chain D: C.477, V.480, A.481, Y.484, S.509, F.513, I.516 Ligands: HEX.40 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.547, C:Y.547 pi-Stacking: C:Y.547 01.34: 14 residues within 4Å: Chain A: C.477, V.480, A.481, Y.484, S.509, F.513, I.516 Chain D: Q.543, L.544, Y.547, S.548, S.551, Y.555 Ligands: HEX.11 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.547, D:Y.547 pi-Stacking: D:Y.547

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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