SMTL ID : 9hl6.1

TRPML1 in complex with compound 4a

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: 8 residues within 4Å: Chain A: R.216, V.236, T.238, V.277, N.278, T.280, L.307, T.309 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.236, A:T.238 NAG-NAG.2: 8 residues within 4Å: Chain B: R.216, V.236, T.238, V.277, N.278, T.280, L.307, T.309 2 PLIP interactions: 2 interactions with chain B Water bridges: B:V.236, B:T.238 NAG-NAG.3: 8 residues within 4Å: Chain C: R.216, V.236, T.238, V.277, N.278, T.280, L.307, T.309 2 PLIP interactions: 2 interactions with chain C Water bridges: C:V.236, C:T.238 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 2 PLIP interactions: 2 interactions with chain D Water bridges: D:V.236, D:T.238

4 x LNK: PENTANE(Non-covalent)

LNK.5: 1 residues within 4Å: Chain A: S.415 No protein-ligand interaction detected (PLIP) LNK.13: 2 residues within 4Å: Chain B: S.415, M.419 No protein-ligand interaction detected (PLIP) LNK.21: 1 residues within 4Å: Chain C: S.415 No protein-ligand interaction detected (PLIP) LNK.27: 1 residues within 4Å: Chain D: S.415 No protein-ligand interaction detected (PLIP)

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

OCT.6: 1 residues within 4Å: Chain A: S.415 No protein-ligand interaction detected (PLIP) OCT.7: 2 residues within 4Å: Chain A: G.401, W.402 No protein-ligand interaction detected (PLIP) OCT.14: 1 residues within 4Å: Chain B: S.415 No protein-ligand interaction detected (PLIP) OCT.15: 2 residues within 4Å: Chain B: G.401, W.402 No protein-ligand interaction detected (PLIP) OCT.22: 1 residues within 4Å: Chain C: S.415 No protein-ligand interaction detected (PLIP) OCT.23: 2 residues within 4Å: Chain C: G.401, W.402 No protein-ligand interaction detected (PLIP) OCT.28: 1 residues within 4Å: Chain D: S.415 No protein-ligand interaction detected (PLIP) OCT.29: 2 residues within 4Å: Chain D: G.401, W.402 No protein-ligand interaction detected (PLIP)

4 x R16: HEXADECANE(Non-covalent)

R16.8: 6 residues within 4Å: Chain A: L.485, S.504, L.505, S.506 Chain D: Q.532 Ligands: 01.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.485, A:L.485, A:L.505 R16.12: 6 residues within 4Å: Chain A: Q.532 Chain C: L.485, S.504, L.505, S.506 Ligands: 01.26 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.485, C:L.485, C:L.505 R16.19: 5 residues within 4Å: Chain B: Q.532 Chain D: L.485, L.505, S.506 Ligands: 01.32 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.485, D:L.485, D:L.505 R16.20: 6 residues within 4Å: Chain B: L.485, S.504, L.505, S.506 Chain C: Q.532 Ligands: 01.18 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.505

4 x HEX: HEXANE(Non-covalent)

HEX.9: 1 residues within 4Å: Chain D: L.537 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.537 HEX.16: 1 residues within 4Å: Chain C: L.537 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.537 HEX.24: 1 residues within 4Å: Chain A: L.537 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.537 HEX.30: 1 residues within 4Å: Chain B: L.537 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.537

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, C.112, K.113, L.359, L.363, R.366, S.367, R.370, Y.403, R.451 18 PLIP interactions: 18 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:R.366, A:S.367, A:S.367 Salt bridges: A:K.103, A:K.107, A:R.109, A:K.113, A:K.113, A:R.366, A:R.366, A:R.370, A:R.451 EUJ.17: 13 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, R.451 18 PLIP interactions: 18 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: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.366, B:R.370, B:R.451 EUJ.25: 13 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, R.451 18 PLIP interactions: 18 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:R.366, C:S.367, C:S.367 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.370, C:R.451 EUJ.31: 13 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, R.451 18 PLIP interactions: 18 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:R.366, D:S.367, D:S.367 Salt bridges: D:K.103, D:K.107, D:R.109, D:K.113, D:K.113, D:R.366, D:R.366, D:R.370, D:R.451

4 x 01: 4-[[(3R)-3-[1-(4-chloranyl-2-fluoranyl-phenyl)piperidin-4-yl]-3-methyl-2H-indol-1-yl]sulfonyl]-N,N-dimethyl-benzenesulfonamide

01.11: 17 residues within 4Å: Chain A: C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.553, V.557, L.558, F.561 Chain D: L.540, Q.543, Y.547, S.551, Y.555 Ligands: R16.8 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:Y.547, D:Y.547, A:V.480, A:V.480, A:Y.484, A:F.513 01.18: 17 residues within 4Å: Chain B: C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.553, V.557, L.558, F.561 Chain C: L.540, Q.543, Y.547, S.551, Y.555 Ligands: R16.20 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:V.480, B:V.480, B:Y.484, B:F.513, C:Y.547, C:Y.547 01.26: 17 residues within 4Å: Chain A: L.540, Q.543, Y.547, S.551, Y.555 Chain C: C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.553, V.557, L.558, F.561 Ligands: R16.12 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:V.480, C:V.480, C:Y.484, C:F.513, A:Y.547, A:Y.547 01.32: 17 residues within 4Å: Chain B: L.540, Q.543, Y.547, S.551, Y.555 Chain D: C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.553, V.557, L.558, F.561 Ligands: R16.19 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:V.480, D:V.480, D:Y.484, D:F.513, B:Y.547, B: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
C

C
B

D
D

Membrane

We predict this structure to be a membrane protein.
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Mucolipin-1

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