SMTL ID : 9hla.1

TRPML1 in complex with compound 9a

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)

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, C.112, K.113, L.359, L.362, L.363, R.366, S.367, R.370, Y.403 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.359, A:L.362, A:L.363 Hydrogen bonds: A:Y.95, A:K.103, A:C.112, A:K.113, A:R.366 Salt bridges: A:K.103, A:K.107, A:R.109, A:K.113, A:K.113, A:R.366, A:R.370 EUJ.18: 13 residues within 4Å: Chain B: Y.95, K.103, K.107, R.109, 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 B Hydrophobic interactions: B:L.359, B:L.362, B:L.363 Hydrogen bonds: B:Y.95, B:K.103, 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.30: 13 residues within 4Å: Chain C: Y.95, K.103, K.107, R.109, C.112, K.113, L.359, L.362, L.363, R.366, S.367, R.370, Y.403 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.359, C:L.362, C:L.363 Hydrogen bonds: C:Y.95, C:K.103, C:C.112, C:K.113, C:R.366 Salt bridges: C:K.103, C:K.107, C:R.109, C:K.113, C:K.113, C:R.366, C:R.370 EUJ.43: 13 residues within 4Å: Chain D: Y.95, K.103, K.107, R.109, C.112, K.113, L.359, L.362, L.363, R.366, S.367, R.370, Y.403 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.359, D:L.362, D:L.363 Hydrogen bonds: D:Y.95, D:K.103, D:C.112, D:K.113, D:R.366 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 HEX: HEXANE(Non-covalent)(Non-functional Binders)

HEX.6: 2 residues within 4Å: Chain A: I.129 Ligands: HEX.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.129 HEX.7: 2 residues within 4Å: Ligands: HEX.6, PLC.52 No protein-ligand interaction detected (PLIP) HEX.8: 2 residues within 4Å: Chain A: C.101, Y.452 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.452 HEX.19: 1 residues within 4Å: Ligands: HEX.20 No protein-ligand interaction detected (PLIP) HEX.20: 2 residues within 4Å: Ligands: PLC.14, HEX.19 No protein-ligand interaction detected (PLIP) HEX.21: 2 residues within 4Å: Chain B: C.101, Y.452 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.452 HEX.31: 2 residues within 4Å: Chain C: I.129 Ligands: HEX.32 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.129 HEX.32: 2 residues within 4Å: Ligands: PLC.27, HEX.31 No protein-ligand interaction detected (PLIP) HEX.33: 2 residues within 4Å: Chain C: C.101, Y.452 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.452 HEX.44: 2 residues within 4Å: Chain D: I.129 Ligands: HEX.45 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.129 HEX.45: 2 residues within 4Å: Ligands: PLC.39, HEX.44 No protein-ligand interaction detected (PLIP) HEX.46: 2 residues within 4Å: Chain D: C.101, Y.452 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.452

4 x D12: DODECANE(Non-covalent)

D12.9: 4 residues within 4Å: Chain A: M.474, R.475, C.478 Chain B: Y.459 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.474 D12.22: 4 residues within 4Å: Chain B: M.474, R.475, C.478 Chain C: Y.459 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:M.474 D12.34: 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 D12.47: 4 residues within 4Å: Chain A: Y.459 Chain D: M.474, R.475, C.478 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:M.474

12 x D10: DECANE(Non-functional Binders)(Non-covalent)

D10.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.11: 2 residues within 4Å: Chain A: S.415, M.419 No protein-ligand interaction detected (PLIP) D10.12: 4 residues within 4Å: Chain A: V.399, G.401, W.402 Ligands: 8K6.42 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.402 D10.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.24: 2 residues within 4Å: Chain B: S.415, M.419 No protein-ligand interaction detected (PLIP) D10.25: 4 residues within 4Å: Chain B: V.399, G.401, W.402 Ligands: 8K6.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.402 D10.35: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.36: 2 residues within 4Å: Chain C: S.415, M.419 No protein-ligand interaction detected (PLIP) D10.37: 4 residues within 4Å: Chain C: V.399, G.401, W.402 Ligands: 8K6.28 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.402 D10.48: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.49: 2 residues within 4Å: Chain D: S.415, M.419 No protein-ligand interaction detected (PLIP) D10.50: 4 residues within 4Å: Chain D: V.399, G.401, W.402 Ligands: 8K6.40 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.402

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

OCT.13: 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 OCT.26: 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 OCT.38: 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 OCT.51: 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

4 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.14: 14 residues within 4Å: Chain A: W.492, R.503, S.504, L.505, S.506, S.509 Chain B: L.133 Chain D: Q.532, W.539, L.540, Q.543, Y.547 Ligands: 01.15, HEX.20 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:L.505, A:S.506, A:S.506, D:Q.532 Hydrophobic interactions: D:W.539, D:Y.547, D:Y.547 PLC.27: 14 residues within 4Å: Chain A: Q.532, W.539, L.540, Q.543, Y.547 Chain B: W.492, R.503, S.504, L.505, S.506, S.509 Chain C: L.133 Ligands: 01.17, HEX.32 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:L.505, B:S.506, B:S.506, A:Q.532 Hydrophobic interactions: A:W.539, A:Y.547, A:Y.547 PLC.39: 15 residues within 4Å: Chain B: Q.532, W.539, L.540, Q.543, Y.547 Chain C: W.492, R.503, S.504, L.505, S.506, S.509 Chain D: L.133, Q.136 Ligands: 01.29, HEX.45 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:L.505, C:S.506, C:S.506, B:Q.532 Hydrophobic interactions: B:W.539, B:Y.547, B:Y.547 PLC.52: 15 residues within 4Å: Chain A: L.133 Chain C: Q.532, W.539, L.540, Q.543, L.544, Y.547 Chain D: W.492, R.503, S.504, L.505, S.506, S.509 Ligands: HEX.7, 01.41 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.539, C:L.544, C:Y.547, C:Y.547 Hydrogen bonds: C:Q.532, D:L.505, D:S.506, D:S.506

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

01.15: 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: PLC.14 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:V.473, A:Y.484, A:I.516, A:F.561, D:Y.547, D:Y.555 Hydrogen bonds: D:S.551 01.17: 17 residues within 4Å: Chain A: Y.547, S.548, S.551, L.552, Y.555, M.556 Chain B: V.473, M.474, C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.561 Ligands: PLC.27 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.547, A:Y.555, A:Y.555, B:V.473, B:Y.484, B:I.516, B:F.561 Hydrogen bonds: A:S.551 01.29: 17 residues within 4Å: Chain B: 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: PLC.39 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:V.473, C:Y.484, C:I.516, C:F.561, B:Y.547, B:Y.555 Hydrogen bonds: B:S.551 01.41: 17 residues within 4Å: Chain C: 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: PLC.52 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:V.473, D:Y.484, D:I.516, D:F.561, C:Y.547, C:Y.555 Hydrogen bonds: C:S.551

4 x 8K6: Octadecane(Non-covalent)

8K6.16: 14 residues within 4Å: Chain A: I.483, Y.487, F.541, L.544, Y.545, S.548, L.552 Chain B: W.402, L.443, V.447, I.450, I.463, R.467 Ligands: D10.25 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.483, A:L.544, B:L.443, B:I.450, B:I.463, B:R.467 8K6.28: 14 residues within 4Å: Chain B: I.483, Y.487, F.541, L.544, Y.545, S.548, L.552 Chain C: W.402, L.443, V.447, I.450, I.463, R.467 Ligands: D10.37 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:I.483, B:L.544, C:L.443, C:I.450, C:I.463, C:R.467 8K6.40: 14 residues within 4Å: Chain C: I.483, Y.487, F.541, L.544, Y.545, S.548, L.552 Chain D: W.402, L.443, V.447, I.450, I.463, R.467 Ligands: D10.50 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.483, C:L.544, D:L.443, D:V.447, D:I.450, D:R.467 8K6.42: 14 residues within 4Å: Chain A: W.402, L.443, V.447, I.450, I.463, R.467 Chain D: I.483, Y.487, F.541, L.544, Y.545, S.548, L.552 Ligands: D10.12 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.443, A:I.450, A:I.463, A:R.467, D:I.483, D:L.544

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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