SMTL ID : 6uza.1

Cryo-EM structure of human TRPC6 in complex with antagonist AM-1473

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x R0G: 4-({(1R,2R)-2-[(3R)-3-aminopiperidin-1-yl]-2,3-dihydro-1H-inden-1-yl}oxy)benzonitrile(Non-covalent)

R0G.1: 10 residues within 4Å: Chain A: K.358, H.362, E.425, E.428, R.525, Y.528, I.529, S.668, Y.669, R.674 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.362, A:E.428, A:Y.528, A:Y.528, A:I.529, A:Y.669 Hydrogen bonds: A:K.358, A:E.425 pi-Stacking: A:H.362 R0G.8: 10 residues within 4Å: Chain B: K.358, H.362, E.425, E.428, R.525, Y.528, I.529, S.668, Y.669, R.674 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.362, B:E.428, B:Y.528, B:Y.528, B:I.529, B:Y.669 Hydrogen bonds: B:K.358, B:E.425 pi-Stacking: B:H.362 R0G.13: 10 residues within 4Å: Chain C: K.358, H.362, E.425, E.428, R.525, Y.528, I.529, S.668, Y.669, R.674 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:H.362, C:E.428, C:Y.528, C:Y.528, C:I.529, C:Y.669 Hydrogen bonds: C:K.358, C:E.425 pi-Stacking: C:H.362 R0G.18: 10 residues within 4Å: Chain D: K.358, H.362, E.425, E.428, R.525, Y.528, I.529, S.668, Y.669, R.674 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:H.362, D:E.428, D:Y.528, D:Y.528, D:I.529, D:Y.669 Hydrogen bonds: D:K.358, D:E.425 pi-Stacking: D:H.362

4 x S9Y: 2-[[(2~{S})-2-decanoyloxypropoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium(Non-covalent)

S9Y.2: 7 residues within 4Å: Chain A: W.442, F.523, A.527, Y.528, Q.540, G.544 Chain B: V.560 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.442, A:A.527, B:V.560 Hydrogen bonds: A:Q.540 pi-Cation interactions: A:W.442 S9Y.9: 7 residues within 4Å: Chain B: W.442, F.523, A.527, Y.528, Q.540, G.544 Chain C: V.560 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.442, B:A.527, C:V.560 Hydrogen bonds: B:Q.540 pi-Cation interactions: B:W.442 S9Y.14: 7 residues within 4Å: Chain C: W.442, F.523, A.527, Y.528, Q.540, G.544 Chain D: V.560 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.442, C:A.527, D:V.560 Hydrogen bonds: C:Q.540 pi-Cation interactions: C:W.442 S9Y.19: 7 residues within 4Å: Chain A: V.560 Chain D: W.442, F.523, A.527, Y.528, Q.540, G.544 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:V.560, D:W.442, D:A.527 Hydrogen bonds: D:Q.540 pi-Cation interactions: D:W.442

4 x SBJ: [(2~{S})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-octanoyloxy-propan-2-yl] octadecanoate(Non-covalent)

SBJ.3: 10 residues within 4Å: Chain A: E.588, F.591, F.595, W.596 Chain B: N.618, Y.621, V.629, T.630, I.633 Ligands: Y01.7 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.621, B:Y.621, B:V.629, B:T.630, B:I.633, A:F.595, A:F.595 Hydrogen bonds: A:E.588 Salt bridges: A:K.592 SBJ.5: 10 residues within 4Å: Chain A: N.618, Y.621, V.629, T.630, I.633 Chain D: E.588, F.591, F.595, W.596 Ligands: Y01.6 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:Y.621, A:Y.621, A:V.629, A:T.630, A:I.633, D:F.595, D:F.595 Hydrogen bonds: D:E.588 Salt bridges: D:K.592 SBJ.10: 10 residues within 4Å: Chain B: E.588, F.591, F.595, W.596 Chain C: N.618, Y.621, V.629, T.630, I.633 Ligands: Y01.12 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:F.595, B:F.595, C:Y.621, C:Y.621, C:V.629, C:T.630, C:I.633 Hydrogen bonds: B:E.588 Salt bridges: B:K.592 SBJ.15: 10 residues within 4Å: Chain C: E.588, F.591, F.595, W.596 Chain D: N.618, Y.621, V.629, T.630, I.633 Ligands: Y01.17 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.621, D:Y.621, D:V.629, D:T.630, D:I.633, C:F.595, C:F.595 Hydrogen bonds: C:E.588 Salt bridges: C:K.592

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 14 residues within 4Å: Chain A: W.307, Y.308, M.319, F.323, F.356, T.367, L.370, V.374, F.523, I.526, I.529, A.532, N.533, W.666 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.323, A:F.356, A:L.370, A:V.374, A:F.523, A:I.526 Salt bridges: A:K.322 Y01.6: 7 residues within 4Å: Chain A: K.614, F.615, N.618, I.619, V.622 Chain D: L.445 Ligands: SBJ.5 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:K.614, A:N.618, A:I.619, A:V.622, D:L.445 Hydrogen bonds: A:N.618 Y01.7: 7 residues within 4Å: Chain A: L.445 Chain B: K.614, F.615, N.618, I.619, V.622 Ligands: SBJ.3 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.445, B:K.614, B:N.618, B:I.619, B:V.622 Hydrogen bonds: B:N.618 Y01.11: 14 residues within 4Å: Chain B: W.307, Y.308, M.319, F.323, F.356, T.367, L.370, V.374, F.523, I.526, I.529, A.532, N.533, W.666 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.323, B:F.356, B:L.370, B:V.374, B:F.523, B:I.526 Salt bridges: B:K.322 Y01.12: 7 residues within 4Å: Chain B: L.445 Chain C: K.614, F.615, N.618, I.619, V.622 Ligands: SBJ.10 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.445, C:K.614, C:N.618, C:I.619, C:V.622 Hydrogen bonds: C:N.618 Y01.16: 14 residues within 4Å: Chain C: W.307, Y.308, M.319, F.323, F.356, T.367, L.370, V.374, F.523, I.526, I.529, A.532, N.533, W.666 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.323, C:F.356, C:L.370, C:V.374, C:F.523, C:I.526 Salt bridges: C:K.322 Y01.17: 7 residues within 4Å: Chain C: L.445 Chain D: K.614, F.615, N.618, I.619, V.622 Ligands: SBJ.15 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:K.614, D:N.618, D:I.619, D:V.622, C:L.445 Hydrogen bonds: D:N.618 Y01.20: 14 residues within 4Å: Chain D: W.307, Y.308, M.319, F.323, F.356, T.367, L.370, V.374, F.523, I.526, I.529, A.532, N.533, W.666 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.323, D:F.356, D:L.370, D:V.374, D:F.523, D:I.526 Salt bridges: D:K.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, Y. et al., Structural basis for pharmacological modulation of the TRPC6 channel. Elife (2020)

Release Date

2020-03-18

Peptides

Short transient receptor potential channel 6: 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 6