SMTL ID : 7wdb.1

Human TRPC5 channel in complex with riluzole

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 9 residues within 4Å: Chain A: A.441, S.444, L.445, A.448, E.470, W.472, I.477, I.484 Ligands: PTY.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.448, A:W.472, A:W.472, A:I.477, A:I.484 Hydrogen bonds: A:E.470 POV.8: 9 residues within 4Å: Chain B: A.441, S.444, L.445, A.448, E.470, W.472, I.477, I.484 Ligands: PTY.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.448, B:W.472, B:W.472, B:I.477, B:I.484 Hydrogen bonds: B:E.470 POV.15: 9 residues within 4Å: Chain C: A.441, S.444, L.445, A.448, E.470, W.472, I.477, I.484 Ligands: PTY.20 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.448, C:W.472, C:W.472, C:I.477, C:I.484 Hydrogen bonds: C:E.470 POV.22: 9 residues within 4Å: Chain D: A.441, S.444, L.445, A.448, E.470, W.472, I.477, I.484 Ligands: PTY.27 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:A.448, D:W.472, D:W.472, D:I.477, D:I.484 Hydrogen bonds: D:E.470

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 11 residues within 4Å: Chain A: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 Chain D: L.526 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:T.371, A:L.375, A:L.493, A:L.496, A:F.497, A:F.497, A:A.499, D:L.526 Hydrogen bonds: A:Y.316, A:N.500 Y01.9: 11 residues within 4Å: Chain B: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 Chain C: L.526 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.371, B:L.375, B:L.493, B:L.496, B:F.497, B:F.497, B:A.499, C:L.526 Hydrogen bonds: B:Y.316, B:N.500 Y01.16: 11 residues within 4Å: Chain A: L.526 Chain C: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:T.371, C:L.375, C:L.493, C:L.496, C:F.497, C:F.497, C:A.499, A:L.526 Hydrogen bonds: C:Y.316, C:N.500 Y01.23: 11 residues within 4Å: Chain B: L.526 Chain D: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain D Hydrophobic interactions: B:L.526, D:T.371, D:L.375, D:L.493, D:L.496, D:F.497, D:F.497, D:A.499 Hydrogen bonds: D:Y.316, D:N.500

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.172, A:C.176, A:C.178, A:C.181 ZN.10: 4 residues within 4Å: Chain B: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.172, B:C.176, B:C.178, B:C.181 ZN.17: 4 residues within 4Å: Chain C: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.172, C:C.176, C:C.178, C:C.181 ZN.24: 4 residues within 4Å: Chain D: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.172, D:C.176, D:C.178, D:C.181

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: E.418, E.421, N.436, D.439, R.492 Ligands: 657.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.418, A:D.439 CA.11: 6 residues within 4Å: Chain B: E.418, E.421, N.436, D.439, R.492 Ligands: 657.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.418, B:D.439 CA.18: 6 residues within 4Å: Chain C: E.418, E.421, N.436, D.439, R.492 Ligands: 657.19 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.418, C:D.439 CA.25: 6 residues within 4Å: Chain D: E.418, E.421, N.436, D.439, R.492 Ligands: 657.26 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.418, D:D.439

4 x 657: 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine(Non-covalent)

657.5: 9 residues within 4Å: Chain A: Y.374, E.418, D.439, N.443, R.492, L.493, S.495, L.496 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.374 Hydrogen bonds: A:N.443, A:R.492 pi-Cation interactions: A:R.492, A:R.492 657.12: 9 residues within 4Å: Chain B: Y.374, E.418, D.439, N.443, R.492, L.493, S.495, L.496 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.374 Hydrogen bonds: B:N.443, B:R.492 pi-Cation interactions: B:R.492, B:R.492 657.19: 9 residues within 4Å: Chain C: Y.374, E.418, D.439, N.443, R.492, L.493, S.495, L.496 Ligands: CA.18 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.374 Hydrogen bonds: C:N.443, C:R.492 pi-Cation interactions: C:R.492, C:R.492 657.26: 9 residues within 4Å: Chain D: Y.374, E.418, D.439, N.443, R.492, L.493, S.495, L.496 Ligands: CA.25 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.374 Hydrogen bonds: D:N.443, D:R.492 pi-Cation interactions: D:R.492, D:R.492

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.6: 13 residues within 4Å: Chain A: W.434, W.435, L.437, M.438, I.484, L.491, I.494, Q.507, G.511 Chain D: T.603, M.604 Ligands: POV.1, 7OC.7 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.434, A:W.435, A:W.435, A:W.435, A:L.437, A:M.438, A:I.484, A:L.491, A:I.494, D:T.603 PTY.13: 13 residues within 4Å: Chain B: W.434, W.435, L.437, M.438, I.484, L.491, I.494, Q.507, G.511 Chain C: T.603, M.604 Ligands: POV.8, 7OC.14 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:T.603, B:W.434, B:W.435, B:W.435, B:W.435, B:L.437, B:M.438, B:I.484, B:L.491, B:I.494 PTY.20: 13 residues within 4Å: Chain A: T.603, M.604 Chain C: W.434, W.435, L.437, M.438, I.484, L.491, I.494, Q.507, G.511 Ligands: POV.15, 7OC.21 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.434, C:W.435, C:W.435, C:W.435, C:L.437, C:M.438, C:I.484, C:L.491, C:I.494, A:T.603 PTY.27: 13 residues within 4Å: Chain B: T.603, M.604 Chain D: W.434, W.435, L.437, M.438, I.484, L.491, I.494, Q.507, G.511 Ligands: POV.22, 7OC.28 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:W.434, D:W.435, D:W.435, D:W.435, D:L.437, D:M.438, D:I.484, D:L.491, D:I.494, B:T.603

4 x 7OC: [3-[(~{E})-octadec-10-enoyl]oxy-2-oxidanyl-propyl] (~{E})-octadec-10-enoate(Non-covalent)

7OC.7: 14 residues within 4Å: Chain A: L.521, Y.524, F.569, Q.573, F.576, W.577 Chain D: F.599, A.602, T.603, G.606, T.607, V.610, V.614 Ligands: PTY.6 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:F.599, D:V.610, D:V.614, A:L.521, A:Y.524, A:Y.524, A:F.569, A:F.576 Hydrogen bonds: A:Q.573 7OC.14: 14 residues within 4Å: Chain B: L.521, Y.524, F.569, Q.573, F.576, W.577 Chain C: F.599, A.602, T.603, G.606, T.607, V.610, V.614 Ligands: PTY.13 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.521, B:Y.524, B:Y.524, B:F.569, B:F.576, C:F.599, C:V.610, C:V.614 Hydrogen bonds: B:Q.573 7OC.21: 14 residues within 4Å: Chain A: F.599, A.602, T.603, G.606, T.607, V.610, V.614 Chain C: L.521, Y.524, F.569, Q.573, F.576, W.577 Ligands: PTY.20 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:L.521, C:Y.524, C:Y.524, C:F.569, C:F.576, A:F.599, A:V.610, A:V.614 Hydrogen bonds: C:Q.573 7OC.28: 14 residues within 4Å: Chain B: F.599, A.602, T.603, G.606, T.607, V.610, V.614 Chain D: L.521, Y.524, F.569, Q.573, F.576, W.577 Ligands: PTY.27 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:F.599, B:V.610, B:V.614, D:L.521, D:Y.524, D:Y.524, D:F.569, D:F.576 Hydrogen bonds: D:Q.573

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Structural identification of riluzole-binding site on human TRPC5. Cell Discov (2022)

Release Date

2022-04-13

Peptides

Short transient receptor potential channel 5: 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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Short transient receptor potential channel 5

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