SMTL ID : 7mgl.1

Structure of human TRPML1 with ML-SI3

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ZB4: N-{(1S,2S)-2-[4-(2-methoxyphenyl)piperazin-1-yl]cyclohexyl}benzenesulfonamide(Non-covalent)

ZB4.1: 14 residues within 4Å: Chain A: V.425, C.429, V.432, A.433, Y.436, I.468, F.505, F.513 Chain D: Y.499, S.500, S.503, Y.507, M.508 Ligands: 3PE.2 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:V.425, A:V.432, A:Y.436, A:I.468, A:F.505, A:F.513, A:F.513, D:Y.499, D:Y.499, D:Y.507, D:Y.507, D:Y.507 ZB4.3: 13 residues within 4Å: Chain A: Y.499, S.503, Y.507, M.508 Chain B: V.425, C.429, V.432, A.433, Y.436, I.468, F.505, F.513 Ligands: 3PE.4 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.425, B:V.432, B:Y.436, B:I.468, B:F.505, B:F.513, B:F.513, A:Y.499, A:Y.499, A:Y.507, A:Y.507, A:Y.507 ZB4.6: 14 residues within 4Å: Chain B: Y.499, S.500, S.503, Y.507, M.508 Chain C: V.425, C.429, V.432, A.433, Y.436, I.468, F.505, F.513 Ligands: 3PE.5 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:V.425, C:V.432, C:Y.436, C:I.468, C:F.505, C:F.513, C:F.513, B:Y.499, B:Y.499, B:Y.507, B:Y.507, B:Y.507 ZB4.7: 13 residues within 4Å: Chain C: Y.499, S.503, Y.507, M.508 Chain D: V.425, C.429, V.432, A.433, Y.436, I.468, F.505, F.513 Ligands: 3PE.8 12 PLIP interactions: 7 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:V.425, D:V.432, D:Y.436, D:I.468, D:F.505, D:F.513, D:F.513, C:Y.499, C:Y.499, C:Y.507, C:Y.507, C:Y.507

4 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.2: 11 residues within 4Å: Chain A: Y.436, L.437, L.457, S.458, S.461 Chain D: Q.484, W.491, Q.495, L.496, Y.499 Ligands: ZB4.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:Y.436, A:L.437, D:Y.499, D:Y.499 Hydrogen bonds: A:S.458 3PE.4: 9 residues within 4Å: Chain A: Q.495, L.496, Y.499 Chain B: Y.436, L.437, L.457, S.458, S.461 Ligands: ZB4.3 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.496, A:Y.499, B:Y.436, B:L.437 Hydrogen bonds: B:S.458 3PE.5: 10 residues within 4Å: Chain B: W.491, Q.495, L.496, Y.499 Chain C: Y.436, L.437, L.457, S.458, S.461 Ligands: ZB4.6 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Y.436, C:L.437, B:L.496, B:Y.499, B:Y.499 Hydrogen bonds: C:S.458 3PE.8: 11 residues within 4Å: Chain C: Q.484, W.491, Q.495, L.496, Y.499 Chain D: Y.436, L.437, L.457, S.458, S.461 Ligands: ZB4.7 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.436, D:L.437, C:Y.499, C:Y.499 Hydrogen bonds: D:S.458

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmiege, P. et al., Atomic insights into ML-SI3 mediated human TRPML1 inhibition. Structure (2021)

Release Date

2021-06-16

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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