SMTL ID : 9hlb.1

TRPML1 in complex with compound 10

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: 6 residues within 4Å: Chain A: R.216, V.236, V.277, N.278, T.280, T.309 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain B: R.216, V.236, V.277, N.278, T.280, T.309 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain C: R.216, V.236, V.277, N.278, T.280, T.309 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain D: R.216, V.236, V.277, N.278, T.280, T.309 No protein-ligand interaction detected (PLIP)

8 x HEX: HEXANE(Non-covalent)(Non-functional Binders)

HEX.5: 2 residues within 4Å: Chain A: F.456, Y.459 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.456, A:F.456 HEX.9: 1 residues within 4Å: Ligands: D12.12 No protein-ligand interaction detected (PLIP) HEX.17: 2 residues within 4Å: Chain B: F.456, Y.459 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.456, B:F.456 HEX.20: 1 residues within 4Å: Ligands: D12.23 No protein-ligand interaction detected (PLIP) HEX.30: 2 residues within 4Å: Chain C: F.456, Y.459 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.456, C:F.456 HEX.33: 1 residues within 4Å: Ligands: D12.36 No protein-ligand interaction detected (PLIP) HEX.40: 2 residues within 4Å: Chain D: F.456, Y.459 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.456, D:F.456 HEX.43: 1 residues within 4Å: Ligands: D12.46 No protein-ligand interaction detected (PLIP)

12 x D12: DODECANE(Non-covalent)

D12.6: 3 residues within 4Å: Chain A: L.122, V.126, I.129 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.126 D12.7: 2 residues within 4Å: Chain A: I.129 Chain D: L.505 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.505, A:I.129 D12.12: 5 residues within 4Å: Chain A: P.471, M.474, R.475, C.478 Ligands: HEX.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.471, A:M.474 D12.15: 1 residues within 4Å: Chain A: L.505 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.505 D12.18: 3 residues within 4Å: Chain B: L.122, V.126, I.129 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.126 D12.23: 5 residues within 4Å: Chain B: P.471, M.474, R.475, C.478 Ligands: HEX.20 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.471, B:M.474 D12.26: 2 residues within 4Å: Chain B: L.505 Chain D: I.129 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:I.129, B:L.505 D12.28: 2 residues within 4Å: Chain B: I.129 Chain C: L.505 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.129, C:L.505 D12.31: 3 residues within 4Å: Chain C: L.122, V.126, I.129 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.126 D12.36: 5 residues within 4Å: Chain C: P.471, M.474, R.475, C.478 Ligands: HEX.33 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.471, C:M.474 D12.41: 3 residues within 4Å: Chain D: L.122, V.126, I.129 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.126 D12.46: 5 residues within 4Å: Chain D: P.471, M.474, R.475, C.478 Ligands: HEX.43 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:P.471, D:M.474

8 x OCT: N-OCTANE(Non-covalent)(Non-functional Binders)

OCT.8: 1 residues within 4Å: Chain A: S.415 No protein-ligand interaction detected (PLIP) OCT.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.19: 1 residues within 4Å: Chain B: S.415 No protein-ligand interaction detected (PLIP) OCT.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.32: 1 residues within 4Å: Chain C: S.415 No protein-ligand interaction detected (PLIP) OCT.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.42: 1 residues within 4Å: Chain D: S.415 No protein-ligand interaction detected (PLIP) OCT.48: 0 residues within 4Å: (No contacts) 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.10: 14 residues within 4Å: Chain A: Y.95, K.103, K.107, R.109, K.110, C.112, K.113, L.359, L.362, L.363, R.366, S.367, R.370, Y.403 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.359, A:L.362, A:L.363 Hydrogen bonds: A:Y.95, A:C.112, A:K.113, A:R.366, A:S.367, A:S.367 Salt bridges: A:K.103, A:K.107, A:R.109, A:K.113, A:K.113, A:R.366, A:R.370 EUJ.21: 14 residues within 4Å: Chain B: Y.95, K.103, K.107, R.109, K.110, C.112, K.113, L.359, L.362, L.363, R.366, S.367, R.370, Y.403 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.359, B:L.362, B:L.363 Hydrogen bonds: B:Y.95, B:C.112, B:K.113, B:R.366, B:S.367, B:S.367 Salt bridges: B:K.103, B:K.107, B:R.109, B:K.113, B:K.113, B:R.366, B:R.370 EUJ.34: 14 residues within 4Å: Chain C: Y.95, K.103, K.107, R.109, K.110, C.112, K.113, L.359, L.362, L.363, R.366, S.367, R.370, Y.403 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.359, C:L.362, C:L.362, C:L.363 Hydrogen bonds: C:Y.95, C:C.112, C:K.113, C:R.366, C:S.367, C:S.367 Salt bridges: C:K.103, C:K.107, C:R.109, C:K.113, C:K.113, C:R.366, C:R.370 EUJ.44: 14 residues within 4Å: Chain D: Y.95, K.103, K.107, R.109, K.110, C.112, K.113, L.359, L.362, L.363, R.366, S.367, R.370, Y.403 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.359, D:L.362, D:L.363 Hydrogen bonds: D:Y.95, D:C.112, D:K.113, D:R.366, D:S.367, D:S.367 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 R16: HEXADECANE(Non-covalent)

R16.11: 7 residues within 4Å: Chain A: Q.532, W.539, Q.543, Y.547 Chain C: S.504, S.506 Ligands: 01.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.539, A:Y.547 R16.22: 7 residues within 4Å: Chain B: Q.532, W.539, Q.543, Y.547 Chain D: S.504, S.506 Ligands: 01.27 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.539, B:Y.547 R16.35: 7 residues within 4Å: Chain B: S.504, S.506 Chain C: Q.532, W.539, Q.543, Y.547 Ligands: 01.29 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.539, C:Y.547 R16.45: 7 residues within 4Å: Chain A: S.504, S.506 Chain D: Q.532, W.539, Q.543, Y.547 Ligands: 01.39 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.539, D:Y.547

4 x D10: DECANE(Non-covalent)

D10.13: 2 residues within 4Å: Chain A: S.415, M.419 No protein-ligand interaction detected (PLIP) D10.24: 2 residues within 4Å: Chain B: S.415, M.419 No protein-ligand interaction detected (PLIP) D10.37: 2 residues within 4Å: Chain C: S.415, M.419 No protein-ligand interaction detected (PLIP) D10.47: 3 residues within 4Å: Chain D: I.414, S.415, M.419 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.414

4 x 01: N-[2-[4-(2-methoxyphenyl)piperazin-1-yl]phenyl]benzenesulfonamide

01.16: 17 residues within 4Å: Chain A: Y.547, S.548, S.551, L.552, Y.555, M.556 Chain C: V.473, M.474, C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.561 Ligands: R16.11 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:V.473, C:V.480, C:I.516, C:F.561, A:Y.547, A:Y.555 pi-Stacking: C:Y.484 Hydrogen bonds: A:S.551 01.27: 17 residues within 4Å: Chain B: Y.547, S.548, S.551, L.552, Y.555, M.556 Chain D: V.473, M.474, C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.561 Ligands: R16.22 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:V.473, D:V.480, D:F.513, D:I.516, D:F.561, B:Y.547, B:Y.555 pi-Stacking: D:Y.484 Hydrogen bonds: B:S.551 01.29: 17 residues within 4Å: Chain B: V.473, M.474, C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.561 Chain C: Y.547, S.548, S.551, L.552, Y.555, M.556 Ligands: R16.35 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:V.473, B:V.480, B:I.516, B:F.561, C:Y.547, C:Y.555 pi-Stacking: B:Y.484 Hydrogen bonds: C:S.551 01.39: 17 residues within 4Å: Chain A: V.473, M.474, C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.561 Chain D: Y.547, S.548, S.551, L.552, Y.555, M.556 Ligands: R16.45 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:Y.547, D:Y.555, A:V.473, A:V.480, A:I.516, A:F.561 Hydrogen bonds: D:S.551 pi-Stacking: A: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
C

C
B

D
D

Membrane

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

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