SMTL ID : 6uz8.1

Cryo-EM structure of human TRPC6 in complex with agonist AM-0883

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x SBM: 2-[[(2~{S})-2-decanoyloxy-3-dodecanoyloxy-propoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium(Non-covalent)

SBM.1: 13 residues within 4Å: Chain A: E.440, W.442, F.523, A.527, Y.528, Q.540, L.543, G.544, V.547 Chain C: M.559, V.629, I.633 Ligands: R0D.9 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:V.629, C:I.633, A:L.543 Hydrogen bonds: A:Q.540 pi-Cation interactions: A:W.442, A:Y.528 SBM.5: 13 residues within 4Å: Chain A: M.559, V.629, I.633 Chain B: E.440, W.442, F.523, A.527, Y.528, Q.540, L.543, G.544, V.547 Ligands: R0D.3 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.629, A:I.633, B:L.543 Hydrogen bonds: B:Q.540 pi-Cation interactions: B:W.442, B:Y.528 SBM.11: 13 residues within 4Å: Chain C: E.440, W.442, F.523, A.527, Y.528, Q.540, L.543, G.544, V.547 Chain D: M.559, V.629, I.633 Ligands: R0D.13 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.543, D:V.629, D:I.633 Hydrogen bonds: C:Q.540 pi-Cation interactions: C:W.442, C:Y.528 SBM.15: 13 residues within 4Å: Chain B: M.559, V.629, I.633 Chain D: E.440, W.442, F.523, A.527, Y.528, Q.540, L.543, G.544, V.547 Ligands: R0D.7 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.543, B:V.629, B:I.633 Hydrogen bonds: D:Q.540 pi-Cation interactions: D:W.442, D:Y.528

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 15 residues within 4Å: Chain A: W.307, Y.308, M.319, K.322, F.323, F.356, A.363, T.367, L.370, F.523, I.526, I.529, A.532, N.533 Chain C: V.562 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.323, A:F.356, A:A.363, A:L.370, A:F.523, A:I.526, C:V.562 Hydrogen bonds: A:Y.308 Salt bridges: A:K.322 Y01.4: 10 residues within 4Å: Chain A: N.612, K.614, F.615, N.618, I.619 Chain B: M.444, L.445, G.448, P.504, I.517 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.614, A:F.615, A:N.618, A:I.619, B:L.445, B:I.517 Hydrogen bonds: A:K.614 Y01.6: 15 residues within 4Å: Chain A: V.562 Chain B: W.307, Y.308, M.319, K.322, F.323, F.356, A.363, T.367, L.370, F.523, I.526, I.529, A.532, N.533 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.323, B:F.356, B:A.363, B:L.370, B:F.523, B:I.526, A:V.562 Hydrogen bonds: B:Y.308 Salt bridges: B:K.322 Y01.8: 9 residues within 4Å: Chain B: K.614, F.615, N.618, I.619 Chain D: M.444, L.445, G.448, P.504, I.517 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:L.445, D:I.517, B:K.614, B:F.615, B:N.618, B:I.619 Hydrogen bonds: B:K.614 Y01.10: 9 residues within 4Å: Chain A: M.444, L.445, G.448, P.504, I.517 Chain C: K.614, F.615, N.618, I.619 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:K.614, C:F.615, C:N.618, C:I.619, A:L.445, A:I.517 Hydrogen bonds: C:K.614 Y01.12: 15 residues within 4Å: Chain C: W.307, Y.308, M.319, K.322, F.323, F.356, A.363, T.367, L.370, F.523, I.526, I.529, A.532, N.533 Chain D: V.562 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.323, C:F.356, C:A.363, C:L.370, C:F.523, C:I.526, D:V.562 Hydrogen bonds: C:Y.308 Salt bridges: C:K.322 Y01.14: 9 residues within 4Å: Chain C: M.444, L.445, G.448, P.504, I.517 Chain D: K.614, F.615, N.618, I.619 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:K.614, D:F.615, D:N.618, D:I.619, C:L.445, C:I.517 Hydrogen bonds: D:K.614 Y01.16: 15 residues within 4Å: Chain B: V.562 Chain D: W.307, Y.308, M.319, K.322, F.323, F.356, A.363, T.367, L.370, F.523, I.526, I.529, A.532, N.533 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:F.323, D:F.356, D:A.363, D:L.370, D:F.523, D:I.526, B:V.562 Hydrogen bonds: D:Y.308 Salt bridges: D:K.322

4 x R0D: (5-chloro-1'H-spiro[indole-3,4'-piperidin]-1'-yl)[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]methanone(Non-covalent)

R0D.3: 10 residues within 4Å: Chain A: N.618, Y.621, V.622, G.625 Chain B: V.587, E.588, F.591, F.595, W.596 Ligands: SBM.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.588, B:F.591, B:F.595 Hydrogen bonds: B:E.588, A:G.625 R0D.7: 10 residues within 4Å: Chain B: N.618, Y.621, V.622, G.625 Chain D: V.587, E.588, F.591, F.595, W.596 Ligands: SBM.15 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:E.588, D:F.591, D:F.595 Hydrogen bonds: D:E.588, B:G.625 R0D.9: 10 residues within 4Å: Chain A: V.587, E.588, F.591, F.595, W.596 Chain C: N.618, Y.621, V.622, G.625 Ligands: SBM.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:E.588, A:F.591, A:F.595 Hydrogen bonds: A:E.588, C:G.625 R0D.13: 10 residues within 4Å: Chain C: V.587, E.588, F.591, F.595, W.596 Chain D: N.618, Y.621, V.622, G.625 Ligands: SBM.11 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:E.588, C:F.591, C:F.595 Hydrogen bonds: C:E.588, D:G.625

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
D

C
B

D
C

Membrane

We predict this structure to be a membrane protein.
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Short transient receptor potential channel 6