SMTL ID : 9hlc.1

TRPML1 in complex with compound 11

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)

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

OCT.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:Y.459 OCT.6: 2 residues within 4Å: Chain A: G.401, W.402 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.402, A:W.402 OCT.14: 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.15: 2 residues within 4Å: Chain B: G.401, W.402 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.402, B:W.402 OCT.21: 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.22: 2 residues within 4Å: Chain C: G.401, W.402 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.402, C:W.402 OCT.29: 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.30: 2 residues within 4Å: Chain D: G.401, W.402 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.402, D:W.402

8 x D12: DODECANE(Non-covalent)

D12.7: 5 residues within 4Å: Chain A: P.471, M.474, R.475, C.478 Chain B: Y.459 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.474 D12.11: 2 residues within 4Å: Chain D: L.505 Ligands: 01.25 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.505 D12.13: 2 residues within 4Å: Chain A: L.505 Ligands: 01.26 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.505 D12.16: 5 residues within 4Å: Chain B: P.471, M.474, R.475, C.478 Chain C: Y.459 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:M.474 D12.20: 2 residues within 4Å: Chain B: L.505 Ligands: 01.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.505 D12.23: 5 residues within 4Å: Chain C: P.471, M.474, R.475, C.478 Chain D: Y.459 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:M.474 D12.28: 2 residues within 4Å: Chain C: L.505 Ligands: 01.18 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.505 D12.31: 5 residues within 4Å: Chain A: Y.459 Chain D: P.471, M.474, R.475, C.478 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:M.474

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: 12 residues within 4Å: Chain A: Y.95, K.103, K.107, R.109, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.359 Hydrogen bonds: A:Y.95, A:Y.95, A:K.103, A:C.112, A:K.113, A:R.366, A:R.366, A:S.367, A:R.370, A:R.370 Salt bridges: A:K.103, A:K.107, A:R.109, A:K.113, A:K.113, A:R.366, A:R.370 EUJ.17: 12 residues within 4Å: Chain B: Y.95, K.103, K.107, R.109, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.359 Hydrogen bonds: B:Y.95, B:Y.95, B:K.103, B:C.112, B:K.113, B:R.366, B:R.366, B:S.367, B:R.370, B:R.370 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: 12 residues within 4Å: Chain C: Y.95, K.103, K.107, R.109, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.359 Hydrogen bonds: C:Y.95, C:Y.95, C:K.103, C:C.112, C:K.113, C:R.366, C:S.367, C:R.370, C:R.370 Salt bridges: C:K.103, C:K.107, C:R.109, C:K.113, C:K.113, C:R.366, C:R.370 EUJ.32: 12 residues within 4Å: Chain D: Y.95, K.103, K.107, R.109, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:L.359 Hydrogen bonds: D:Y.95, D:Y.95, D:K.103, D:C.112, D:K.113, D:R.366, D:R.366, D:S.367, D:R.370, D:R.370 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: (8R,9S,13S,14S,17S)-3-methoxy-13-methyl-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-17-ol

01.9: 13 residues within 4Å: Chain A: Y.547, S.551, Y.555 Chain B: C.477, V.480, A.481, Y.484, L.485, L.505, S.509, F.513 Ligands: 8K6.12, D12.20 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.547, A:Y.547, B:A.481, B:Y.484, B:Y.484, B:L.485, B:F.513 01.18: 13 residues within 4Å: Chain B: Y.547, S.551, Y.555 Chain C: C.477, V.480, A.481, Y.484, L.485, L.505, S.509, F.513 Ligands: 8K6.19, D12.28 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:Y.547, B:Y.547, C:A.481, C:Y.484, C:Y.484, C:L.485, C:F.513 01.25: 13 residues within 4Å: Chain C: Y.547, S.551, Y.555 Chain D: C.477, V.480, A.481, Y.484, L.485, L.505, S.509, F.513 Ligands: D12.11, 8K6.27 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.481, D:Y.484, D:Y.484, D:L.485, D:F.513, C:Y.547, C:Y.547 01.26: 13 residues within 4Å: Chain A: C.477, V.480, A.481, Y.484, L.485, L.505, S.509, F.513 Chain D: Y.547, S.551, Y.555 Ligands: 8K6.10, D12.13 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:A.481, A:Y.484, A:Y.484, A:L.485, A:F.513, D:Y.547, D:Y.547

4 x 8K6: Octadecane(Non-covalent)

8K6.10: 7 residues within 4Å: Chain A: S.504, S.506 Chain D: Q.532, Q.543, Y.547, S.551 Ligands: 01.26 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.547, D:Y.547 8K6.12: 7 residues within 4Å: Chain A: Q.532, Q.543, Y.547, S.551 Chain B: S.504, S.506 Ligands: 01.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.547, A:Y.547 8K6.19: 7 residues within 4Å: Chain B: Q.532, Q.543, Y.547, S.551 Chain C: S.504, S.506 Ligands: 01.18 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.547, B:Y.547 8K6.27: 7 residues within 4Å: Chain C: Q.532, Q.543, Y.547, S.551 Chain D: S.504, S.506 Ligands: 01.25 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.547, C: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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