SMTL ID : 7d4q.1

Structure of human TRPC5 in complex with HC-070

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 14 residues within 4Å: Chain A: W.434, W.435, M.438, I.484, L.491, I.494, L.510, L.514 Chain D: I.523, F.531, T.603, M.604, T.607 Ligands: POV.2 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:F.531, D:T.603, D:T.607, A:W.435, A:M.438, A:I.484, A:L.491 PTY.7: 14 residues within 4Å: Chain A: I.523, F.531, T.603, M.604, T.607 Chain B: W.434, W.435, M.438, I.484, L.491, I.494, L.510, L.514 Ligands: POV.8 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.531, A:T.603, A:T.607, B:W.435, B:M.438, B:I.484, B:L.491 PTY.13: 14 residues within 4Å: Chain B: I.523, F.531, T.603, M.604, T.607 Chain C: W.434, W.435, M.438, I.484, L.491, I.494, L.510, L.514 Ligands: POV.14 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.435, C:M.438, C:I.484, C:L.491, B:F.531, B:T.603, B:T.607 PTY.19: 14 residues within 4Å: Chain C: I.523, F.531, T.603, M.604, T.607 Chain D: W.434, W.435, M.438, I.484, L.491, I.494, L.510, L.514 Ligands: POV.20 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.531, C:T.603, C:T.607, D:W.435, D:M.438, D:I.484, D:L.491

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

POV.2: 7 residues within 4Å: Chain A: S.444, E.470, W.472, I.477, L.481, I.484 Ligands: PTY.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.472, A:W.472, A:I.477, A:L.481, A:L.481, A:I.484 Hydrogen bonds: A:E.470 POV.8: 7 residues within 4Å: Chain B: S.444, E.470, W.472, I.477, L.481, I.484 Ligands: PTY.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.472, B:W.472, B:I.477, B:L.481, B:L.481, B:I.484 Hydrogen bonds: B:E.470 POV.14: 7 residues within 4Å: Chain C: S.444, E.470, W.472, I.477, L.481, I.484 Ligands: PTY.13 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.472, C:W.472, C:I.477, C:L.481, C:L.481, C:I.484 Hydrogen bonds: C:E.470 POV.20: 7 residues within 4Å: Chain D: S.444, E.470, W.472, I.477, L.481, I.484 Ligands: PTY.19 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.472, D:W.472, D:I.477, D:L.481, D:L.481, D:I.484 Hydrogen bonds: D:E.470

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 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 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:T.371, A:L.493, A:F.497, A:F.497, D:L.526 Hydrogen bonds: A:Y.316, A:A.499, A:N.500 Y01.9: 11 residues within 4Å: Chain A: L.526 Chain B: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.371, B:L.493, B:F.497, B:F.497, A:L.526 Hydrogen bonds: B:Y.316, B:A.499, B:N.500 Y01.15: 11 residues within 4Å: Chain B: L.526 Chain C: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.371, C:L.493, C:F.497, C:F.497, B:L.526 Hydrogen bonds: C:Y.316, C:A.499, C:N.500 Y01.21: 11 residues within 4Å: Chain C: L.526 Chain D: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:T.371, D:L.493, D:F.497, D:F.497, C:L.526 Hydrogen bonds: D:Y.316, D:A.499, D:N.500

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.16: 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.22: 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.5: 5 residues within 4Å: Chain A: E.418, E.421, N.436, D.439, R.492 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.439 CA.11: 5 residues within 4Å: Chain B: E.418, E.421, N.436, D.439, R.492 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.439 CA.17: 5 residues within 4Å: Chain C: E.418, E.421, N.436, D.439, R.492 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.439 CA.23: 5 residues within 4Å: Chain D: E.418, E.421, N.436, D.439, R.492 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.439

4 x GWR: 8-(3-chloranylphenoxy)-7-[(4-chlorophenyl)methyl]-3-methyl-1-(3-oxidanylpropyl)purine-2,6-dione(Non-covalent)

GWR.6: 13 residues within 4Å: Chain A: L.521, C.525, R.557, F.569, L.572, Q.573, F.576, W.577 Chain D: F.599, A.602, T.603, G.606, T.607 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.521, A:F.569, A:L.572, A:L.572 Hydrogen bonds: A:R.557, A:Q.573, D:T.607 pi-Stacking: A:F.576 GWR.12: 13 residues within 4Å: Chain A: F.599, A.602, T.603, G.606, T.607 Chain B: L.521, C.525, R.557, F.569, L.572, Q.573, F.576, W.577 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:T.607, B:R.557, B:Q.573 Hydrophobic interactions: B:L.521, B:F.569, B:L.572, B:L.572 pi-Stacking: B:F.576 GWR.18: 13 residues within 4Å: Chain B: F.599, A.602, T.603, G.606, T.607 Chain C: L.521, C.525, R.557, F.569, L.572, Q.573, F.576, W.577 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.521, C:F.569, C:L.572, C:L.572 Hydrogen bonds: C:R.557, C:Q.573, B:T.607 pi-Stacking: C:F.576 GWR.24: 13 residues within 4Å: Chain C: F.599, A.602, T.603, G.606, T.607 Chain D: L.521, C.525, R.557, F.569, L.572, Q.573, F.576, W.577 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.521, D:F.569, D:L.572, D:L.572 Hydrogen bonds: D:R.557, D:Q.573, C:T.607 pi-Stacking: D:F.576

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, K. et al., Structural basis for human TRPC5 channel inhibition by two distinct inhibitors. Elife (2021)

Release Date

2021-03-31

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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