SMTL ID : 9hl4.1

TRPML1 in complex with compound 3

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 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain B: R.216, V.236, T.238, V.277, N.278, T.280, T.309 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain C: R.216, V.236, T.238, V.277, N.278, T.280, T.309 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain D: R.216, V.236, T.238, V.277, N.278, T.280, T.309 No protein-ligand interaction detected (PLIP)

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

OCT.5: 1 residues within 4Å: Chain A: S.415 No protein-ligand interaction detected (PLIP) OCT.6: 1 residues within 4Å: Chain A: L.437 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.437 OCT.14: 1 residues within 4Å: Chain B: S.415 No protein-ligand interaction detected (PLIP) OCT.15: 1 residues within 4Å: Chain B: L.437 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.437 OCT.21: 1 residues within 4Å: Chain C: S.415 No protein-ligand interaction detected (PLIP) OCT.22: 1 residues within 4Å: Chain C: L.437 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.437 OCT.29: 1 residues within 4Å: Chain D: S.415 No protein-ligand interaction detected (PLIP) OCT.30: 1 residues within 4Å: Chain D: L.437 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.437

8 x D10: DECANE(Non-covalent)

D10.7: 6 residues within 4Å: Chain A: S.504, L.505, S.506 Chain D: Q.532, Q.543 Ligands: D10.28 No protein-ligand interaction detected (PLIP) D10.11: 6 residues within 4Å: Chain A: Q.532, Q.543 Chain B: S.504, L.505, S.506 Ligands: D10.12 No protein-ligand interaction detected (PLIP) D10.12: 6 residues within 4Å: Chain A: Y.547, S.548, S.551, L.552 Ligands: D10.11, 01.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.547, A:Y.547 D10.18: 6 residues within 4Å: Chain B: Q.532, Q.543 Chain C: S.504, L.505, S.506 Ligands: D10.19 No protein-ligand interaction detected (PLIP) D10.19: 6 residues within 4Å: Chain B: Y.547, S.548, S.551, L.552 Ligands: D10.18, 01.20 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.547, B:Y.547 D10.25: 6 residues within 4Å: Chain C: Q.532, Q.543 Chain D: S.504, L.505, S.506 Ligands: D10.26 No protein-ligand interaction detected (PLIP) D10.26: 6 residues within 4Å: Chain C: Y.547, S.548, S.551, L.552 Ligands: D10.25, 01.27 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.547, C:Y.547 D10.28: 6 residues within 4Å: Chain D: Y.547, S.548, S.551, L.552 Ligands: D10.7, 01.10 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.547, D:Y.547

4 x R16: HEXADECANE(Non-covalent)

R16.8: 4 residues within 4Å: Chain A: F.456, Y.459 Chain D: C.478, L.485 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.456, A:F.456, A:F.456, A:Y.459, A:Y.459, D:L.485 R16.16: 4 residues within 4Å: Chain A: C.478, L.485 Chain B: F.456, Y.459 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.485, B:F.456, B:F.456, B:F.456, B:Y.459, B:Y.459 R16.23: 4 residues within 4Å: Chain B: C.478, L.485 Chain C: F.456, Y.459 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.456, C:F.456, C:F.456, C:Y.459, C:Y.459, B:L.485 R16.31: 4 residues within 4Å: Chain C: C.478, L.485 Chain D: F.456, Y.459 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.456, D:F.456, D:F.456, D:Y.459, D:Y.459, C:L.485

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.9: 13 residues within 4Å: Chain A: Y.95, K.103, K.107, R.109, K.110, C.112, K.113, L.363, R.366, S.367, R.370, Y.403, R.451 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.103, A:C.112, A:K.113, A:R.366, A:S.367, A:S.367, 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.370 EUJ.17: 13 residues within 4Å: Chain B: Y.95, K.103, K.107, R.109, K.110, C.112, K.113, L.363, R.366, S.367, R.370, Y.403, R.451 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:K.103, B:C.112, B:K.113, B:R.366, B:S.367, 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.370 EUJ.24: 13 residues within 4Å: Chain C: Y.95, K.103, K.107, R.109, K.110, C.112, K.113, L.363, R.366, S.367, R.370, Y.403, R.451 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:K.103, C:C.112, C:K.113, C:R.366, C:S.367, 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.370 EUJ.32: 13 residues within 4Å: Chain D: Y.95, K.103, K.107, R.109, K.110, C.112, K.113, L.363, R.366, S.367, R.370, Y.403, R.451 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:K.103, D:C.112, D:K.113, D:R.366, D:S.367, D:S.367, 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.370

4 x 01: N4-[2-[4-(4-chloranyl-2-fluoranyl-phenyl)piperazin-1-yl]phenyl]-N1,N1-dimethyl-benzene-1,4-disulfonamide

01.10: 20 residues within 4Å: Chain A: L.466, L.470, 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: D10.28 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.473, A:V.480, A:V.480, A:F.513, A:F.513, A:F.561, D:Y.547 pi-Stacking: A:Y.484 01.13: 20 residues within 4Å: Chain A: Y.547, S.551, Y.555, M.556 Chain B: L.466, L.470, 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: D10.12 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.473, B:V.480, B:V.480, B:F.513, B:F.513, B:F.561, A:Y.547 pi-Stacking: B:Y.484 01.20: 20 residues within 4Å: Chain B: Y.547, S.551, Y.555, M.556 Chain C: L.466, L.470, 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: D10.19 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.473, C:V.480, C:V.480, C:F.513, C:F.513, C:F.561, B:Y.547 pi-Stacking: C:Y.484 01.27: 20 residues within 4Å: Chain C: Y.547, S.551, Y.555, M.556 Chain D: L.466, L.470, 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: D10.26 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:Y.547, D:V.473, D:V.480, D:V.480, D:F.513, D:F.513, D:F.561 pi-Stacking: D: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
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Mucolipin-1

Related Entries With Identical Sequence