SMTL ID : 9hj6.1

TRPML1 in complex with compound 2

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: 15 residues within 4Å: Chain A: Y.95, K.103, K.107, R.109, K.110, P.111, 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, A:L.359 Hydrogen bonds: A:K.103, A:C.112, A:K.113, A:R.366, A:R.366, 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.366, A:R.370 EUJ.13: 15 residues within 4Å: Chain B: Y.95, K.103, K.107, R.109, K.110, P.111, 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:K.103, B:C.112, B:K.113, B:R.366, 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, B:R.370 EUJ.20: 15 residues within 4Å: Chain C: Y.95, K.103, K.107, R.109, K.110, P.111, 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:K.103, C:C.112, C:K.113, C:R.366, 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.370 EUJ.27: 15 residues within 4Å: Chain D: Y.95, K.103, K.107, R.109, K.110, P.111, 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:K.103, D:C.112, D:K.113, D:R.366, D:R.366, 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.366, D:R.370

4 x 01: N4-(3-chloranyl-2-piperidin-1-yl-phenyl)-N1,N1-dimethyl-benzene-1,4-disulfonamide

01.6: 15 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: Y.547, S.551, Y.555 Ligands: R16.30 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.480, A:V.480, A:Y.484, A:F.513, A:F.561, D:Y.547 01.12: 15 residues within 4Å: Chain A: Y.547, S.551, Y.555 Chain B: C.477, V.480, A.481, Y.484, S.509, F.513, I.516, F.553, V.557, L.558, F.561 Ligands: R16.9 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.480, B:V.480, B:Y.484, B:F.513, B:F.561, A:Y.547 01.19: 15 residues within 4Å: Chain B: 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: R16.16 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.480, C:V.480, C:Y.484, C:F.513, C:F.561, B:Y.547 01.26: 15 residues within 4Å: Chain C: 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: R16.23 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.561, C:Y.547 pi-Stacking: D:Y.484

8 x HEX: HEXANE(Non-covalent)

HEX.7: 4 residues within 4Å: Chain A: C.101, L.114, Y.452, F.456 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.114, A:Y.452, A:F.456 HEX.8: 3 residues within 4Å: Chain A: L.453, F.456, Y.459 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.453, A:F.456 HEX.14: 4 residues within 4Å: Chain B: C.101, L.114, Y.452, F.456 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.114, B:Y.452, B:F.456 HEX.15: 3 residues within 4Å: Chain B: L.453, F.456, Y.459 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.453, B:F.456 HEX.21: 4 residues within 4Å: Chain C: C.101, L.114, Y.452, F.456 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.114, C:Y.452, C:F.456 HEX.22: 3 residues within 4Å: Chain C: L.453, F.456, Y.459 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.453, C:F.456 HEX.28: 4 residues within 4Å: Chain D: C.101, L.114, Y.452, F.456 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.114, D:Y.452, D:F.456 HEX.29: 3 residues within 4Å: Chain D: L.453, F.456, Y.459 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.453, D:F.456

4 x R16: HEXADECANE(Non-covalent)

R16.9: 4 residues within 4Å: Chain A: Q.532, Y.547 Chain B: S.506 Ligands: 01.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.547 R16.16: 4 residues within 4Å: Chain B: Q.532, Y.547 Chain C: S.506 Ligands: 01.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.547 R16.23: 4 residues within 4Å: Chain C: Q.532, Y.547 Chain D: S.506 Ligands: 01.26 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.547 R16.30: 4 residues within 4Å: Chain A: S.506 Chain D: Q.532, Y.547 Ligands: 01.6 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.547

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

OCT.10: 3 residues within 4Å: Chain A: V.399, G.401, W.402 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.402 OCT.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.17: 3 residues within 4Å: Chain B: V.399, G.401, W.402 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.402 OCT.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.24: 3 residues within 4Å: Chain C: V.399, G.401, W.402 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.402 OCT.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.31: 3 residues within 4Å: Chain D: V.399, G.401, W.402 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.402 OCT.32: 0 residues within 4Å: (No contacts) 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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