SMTL ID : 9hj8.1

TRPML1 in complex with compound 5

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: 8 residues within 4Å: Chain D: R.216, V.236, T.238, 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: 14 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, R.451 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.359 Hydrogen bonds: A:Y.95, A:K.103, A:C.112, A:K.113, A:R.366, A:S.367, A:S.367, A:R.370, 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.10: 14 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, R.451 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.359 Hydrogen bonds: B:Y.95, B:K.103, B:C.112, B:K.113, B:R.366, B:S.367, B:S.367, B:R.370, 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.15: 14 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, R.451 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.359 Hydrogen bonds: C:Y.95, C:K.103, C:C.112, C:K.113, C:R.366, C:S.367, C:S.367, C:R.370, 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 EUJ.20: 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 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.359 Hydrogen bonds: D:Y.95, D:K.103, D:C.112, D:K.113, D:R.366, D:S.367, D:S.367, D:R.370, 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: N,N-dimethyl-4-[1'-[2,2,2-tris(fluoranyl)ethyl]spiro[2H-indole-3,4'-piperidine]-1-yl]sulfonyl-benzenesulfonamide

01.6: 18 residues within 4Å: Chain A: V.473, M.474, C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.553, V.557, L.558, F.561 Chain D: Y.547, S.551, Y.555, M.556 Ligands: PC1.7 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.480, A:V.480, A:F.513, A:F.513, D:Y.547 pi-Stacking: A:Y.484 01.11: 18 residues within 4Å: Chain A: Y.547, S.551, 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.553, V.557, L.558, F.561 Ligands: PC1.12 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.480, B:V.480, B:F.513, B:F.513, A:Y.547 pi-Stacking: B:Y.484 01.16: 18 residues within 4Å: Chain B: Y.547, S.551, 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.553, V.557, L.558, F.561 Ligands: PC1.17 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.480, C:V.480, C:F.513, C:F.513, B:Y.547 pi-Stacking: C:Y.484 01.21: 18 residues within 4Å: Chain C: Y.547, S.551, 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.553, V.557, L.558, F.561 Ligands: PC1.22 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.480, D:V.480, D:F.513, D:F.513, C:Y.547 pi-Stacking: D:Y.484

4 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.7: 14 residues within 4Å: Chain A: M.474, C.478, L.485, W.492, R.503, S.504, L.505, S.506, S.509 Chain D: Q.532, W.539, Q.543, Y.547 Ligands: 01.6 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.547, D:Y.547, A:M.474, A:L.485 Hydrogen bonds: D:Q.532, A:S.506 PC1.12: 14 residues within 4Å: Chain A: Q.532, W.539, Q.543, Y.547 Chain B: M.474, C.478, L.485, W.492, R.503, S.504, L.505, S.506, S.509 Ligands: 01.11 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:M.474, B:L.485, A:Y.547, A:Y.547 Hydrogen bonds: B:S.506, A:Q.532 PC1.17: 14 residues within 4Å: Chain B: Q.532, W.539, Q.543, Y.547 Chain C: M.474, C.478, L.485, W.492, R.503, S.504, L.505, S.506, S.509 Ligands: 01.16 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:M.474, C:L.485, B:Y.547, B:Y.547 Hydrogen bonds: C:S.506, B:Q.532 PC1.22: 14 residues within 4Å: Chain C: Q.532, W.539, Q.543, Y.547 Chain D: M.474, C.478, L.485, W.492, R.503, S.504, L.505, S.506, S.509 Ligands: 01.21 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:M.474, D:L.485, C:Y.547, C:Y.547 Hydrogen bonds: D:S.506, C:Q.532

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

OCT.8: 3 residues within 4Å: Chain A: G.401, W.402, R.467 No protein-ligand interaction detected (PLIP) OCT.9: 2 residues within 4Å: Chain A: S.415, M.419 No protein-ligand interaction detected (PLIP) OCT.13: 3 residues within 4Å: Chain B: G.401, W.402, R.467 No protein-ligand interaction detected (PLIP) OCT.14: 2 residues within 4Å: Chain B: S.415, M.419 No protein-ligand interaction detected (PLIP) OCT.18: 3 residues within 4Å: Chain C: G.401, W.402, R.467 No protein-ligand interaction detected (PLIP) OCT.19: 2 residues within 4Å: Chain C: S.415, M.419 No protein-ligand interaction detected (PLIP) OCT.23: 3 residues within 4Å: Chain D: G.401, W.402, R.467 No protein-ligand interaction detected (PLIP) OCT.24: 2 residues within 4Å: Chain D: S.415, M.419 No protein-ligand interaction detected (PLIP)

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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