SMTL ID : 9hld.1

TRPML1 in complex with compound 13

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

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

OCT.5: 2 residues within 4Å: Chain A: F.456, Y.459 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.456, A:F.456, A:Y.459 OCT.13: 3 residues within 4Å: Chain B: L.453, F.456, Y.459 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.453, B:F.456, B:F.456, B:Y.459 OCT.21: 3 residues within 4Å: Chain C: L.453, F.456, Y.459 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.453, C:F.456, C:F.456, C:Y.459 OCT.30: 2 residues within 4Å: Chain D: F.456, Y.459 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.456, D:F.456, D:Y.459

4 x D12: DODECANE(Non-covalent)

D12.6: 6 residues within 4Å: Chain A: W.393, P.471, M.474, R.475, C.478 Chain B: Y.459 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.393, A:P.471, A:P.471, A:M.474, A:R.475 D12.14: 6 residues within 4Å: Chain B: W.393, P.471, M.474, R.475, C.478 Chain C: Y.459 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.393, B:P.471, B:P.471, B:M.474, B:R.475 D12.22: 6 residues within 4Å: Chain C: W.393, P.471, M.474, R.475, C.478 Chain D: Y.459 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.393, C:P.471, C:P.471, C:M.474, C:R.475 D12.31: 6 residues within 4Å: Chain A: Y.459 Chain D: W.393, P.471, M.474, R.475, C.478 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.393, D:P.471, D:P.471, D:M.474, D:R.475

4 x D10: DECANE(Non-covalent)

D10.7: 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 D10.15: 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 D10.23: 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 D10.32: 3 residues within 4Å: Chain D: G.401, W.402, L.405 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.402, D:W.402, D:L.405

4 x 8K6: Octadecane(Non-covalent)

8K6.8: 6 residues within 4Å: Chain A: W.539, Q.543, Y.547 Chain B: S.504, S.506 Ligands: 01.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.539, A:Y.547, A:Y.547 8K6.16: 6 residues within 4Å: Chain B: W.539, Q.543, Y.547 Chain C: S.504, S.506 Ligands: 01.20 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.539, B:Y.547, B:Y.547 8K6.24: 6 residues within 4Å: Chain C: W.539, Q.543, Y.547 Chain D: S.504, S.506 Ligands: 01.28 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.539, C:Y.547, C:Y.547 8K6.33: 6 residues within 4Å: Chain A: S.504, S.506 Chain D: W.539, Q.543, Y.547 Ligands: 01.29 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.539, D:Y.547, D:Y.547

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

HEX.9: 1 residues within 4Å: Chain A: I.129 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.129 HEX.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.17: 1 residues within 4Å: Chain B: I.129 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.129 HEX.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.25: 1 residues within 4Å: Chain C: I.129 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.129 HEX.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.34: 1 residues within 4Å: Chain D: I.129 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.129 HEX.36: 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: 13 residues within 4Å: Chain A: Y.95, K.103, K.107, R.109, K.110, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.103, A:K.103, A:C.112, A:K.113, A:R.366, A:S.367, A:R.370, 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.366 EUJ.18: 13 residues within 4Å: Chain B: Y.95, K.103, K.107, R.109, K.110, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.103, B:C.112, B:K.113, B:R.366, 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.366 EUJ.26: 13 residues within 4Å: Chain C: Y.95, K.103, K.107, R.109, K.110, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:K.103, C:K.103, C:C.112, C:K.113, C:R.366, 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.366, C:R.366 EUJ.35: 14 residues within 4Å: Chain D: Y.95, K.103, K.107, R.109, K.110, 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 Hydrogen bonds: D:K.103, D:K.103, D:C.112, D:K.113, D:R.366, D:S.367, D:R.370, 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.366

4 x 01: 1-[(8R,9S,13S,14S,17S)-13-methyl-17-oxidanyl-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-3-yl]ethanone

01.12: 14 residues within 4Å: Chain A: Y.547, S.551, Y.555 Chain B: C.477, V.480, A.481, Y.484, L.485, C.488, L.505, S.506, S.509, F.513 Ligands: 8K6.8 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.484, B:Y.484, B:L.485, B:F.513, A:Y.547, A:Y.547 Hydrogen bonds: A:S.551, A:S.551, A:Y.555 01.20: 14 residues within 4Å: Chain B: Y.547, S.551, Y.555 Chain C: C.477, V.480, A.481, Y.484, L.485, C.488, L.505, S.506, S.509, F.513 Ligands: 8K6.16 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.547, B:Y.547, C:Y.484, C:Y.484, C:L.485, C:F.513 Hydrogen bonds: B:S.551, B:S.551, B:Y.555 01.28: 14 residues within 4Å: Chain C: Y.547, S.551, Y.555 Chain D: C.477, V.480, A.481, Y.484, L.485, C.488, L.505, S.506, S.509, F.513 Ligands: 8K6.24 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:Y.484, D:Y.484, D:L.485, D:F.513, C:Y.547, C:Y.547 Hydrogen bonds: C:S.551, C:S.551, C:Y.555 01.29: 14 residues within 4Å: Chain A: C.477, V.480, A.481, Y.484, L.485, C.488, L.505, S.506, S.509, F.513 Chain D: Y.547, S.551, Y.555 Ligands: 8K6.33 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.547, D:Y.547, A:Y.484, A:L.485, A:F.513 Hydrogen bonds: D:S.551, D:S.551, D:Y.555

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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