SMTL ID : 7dxg.1

Structure of SAR7334-bound TRPC6 at 2.9 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.249, C.253, C.255, C.258 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.249, A:C.255, A:C.258 ZN.12: 4 residues within 4Å: Chain B: H.249, C.253, C.255, C.258 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.249, B:C.255, B:C.258 ZN.24: 4 residues within 4Å: Chain C: H.249, C.253, C.255, C.258 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.249, C:C.255, C:C.258 ZN.33: 4 residues within 4Å: Chain D: H.249, C.253, C.255, C.258 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.249, D:C.255, D:C.258

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: E.144, D.890 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.144, A:E.144, A:D.890 CA.5: 4 residues within 4Å: Chain A: E.878, N.880, E.883 Chain D: E.881 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Metal complexes: A:E.883, D:E.881 CA.13: 2 residues within 4Å: Chain B: E.144, D.890 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.144, B:E.144, B:D.890 CA.16: 4 residues within 4Å: Chain B: E.878, N.880, E.883 Chain C: E.881 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:E.883, C:E.881 CA.25: 2 residues within 4Å: Chain C: E.144, D.890 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.144, C:E.144, C:D.890 CA.28: 4 residues within 4Å: Chain A: E.881 Chain C: E.878, N.880, E.883 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:E.883, A:E.881 CA.34: 2 residues within 4Å: Chain D: E.144, D.890 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.144, D:E.144, D:D.890 CA.37: 4 residues within 4Å: Chain B: E.881 Chain D: E.878, N.880, E.883 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:E.883, B:E.881

16 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 17 residues within 4Å: Chain A: W.391, Y.392, M.403, K.406, F.407, V.410, F.440, F.443, A.447, T.451, L.454, V.458, F.607, I.613, A.616, N.617 Ligands: POV.39 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.407, A:F.407, A:V.410, A:V.410, A:F.443, A:A.447, A:L.454, A:V.458, A:F.607, A:I.613, A:A.616 Salt bridges: A:K.406 Y01.6: 8 residues within 4Å: Chain A: M.528, G.532, A.535, A.539, I.594 Chain D: F.699 Ligands: Y01.8, Y01.32 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.535, A:A.539 Y01.8: 8 residues within 4Å: Chain A: F.531, A.539, I.542, A.543, M.546, S.589, I.594 Ligands: Y01.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.531, A:A.539, A:I.542, A:A.543 Y01.10: 11 residues within 4Å: Chain A: K.698, F.699, N.702, I.703, V.706 Chain C: L.529, I.536, I.601, L.605 Ligands: Y01.29, POV.30 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.529, C:I.536, C:I.601, C:L.605, A:F.699, A:I.703, A:V.706 Hydrogen bonds: A:N.702 Y01.14: 17 residues within 4Å: Chain B: W.391, Y.392, M.403, K.406, F.407, V.410, F.440, F.443, A.447, T.451, L.454, V.458, F.607, I.613, A.616, N.617 Ligands: POV.30 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.407, B:F.407, B:V.410, B:V.410, B:F.443, B:A.447, B:L.454, B:V.458, B:F.607, B:I.613, B:A.616 Salt bridges: B:K.406 Y01.17: 8 residues within 4Å: Chain B: M.528, G.532, A.535, A.539, I.594 Chain C: F.699 Ligands: Y01.19, Y01.23 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.535, B:A.539 Y01.19: 8 residues within 4Å: Chain B: F.531, A.539, I.542, A.543, M.546, S.589, I.594 Ligands: Y01.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.531, B:A.539, B:I.542, B:A.543 Y01.21: 11 residues within 4Å: Chain B: K.698, F.699, N.702, I.703, V.706 Chain D: L.529, I.536, I.601, L.605 Ligands: Y01.38, POV.39 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:L.529, D:I.536, D:I.601, D:L.605, B:F.699, B:I.703, B:V.706 Hydrogen bonds: B:N.702 Y01.23: 11 residues within 4Å: Chain B: L.529, I.536, I.601, L.605 Chain C: K.698, F.699, N.702, I.703, V.706 Ligands: Y01.17, POV.18 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.699, C:I.703, C:V.706, B:L.529, B:I.536, B:I.601, B:L.605 Hydrogen bonds: C:N.702 Y01.26: 17 residues within 4Å: Chain C: W.391, Y.392, M.403, K.406, F.407, V.410, F.440, F.443, A.447, T.451, L.454, V.458, F.607, I.613, A.616, N.617 Ligands: POV.7 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.407, C:F.407, C:V.410, C:V.410, C:F.443, C:A.447, C:L.454, C:V.458, C:F.607, C:I.613, C:A.616 Salt bridges: C:K.406 Y01.29: 8 residues within 4Å: Chain A: F.699 Chain C: M.528, G.532, A.535, A.539, I.594 Ligands: Y01.10, Y01.31 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.535, C:A.539 Y01.31: 8 residues within 4Å: Chain C: F.531, A.539, I.542, A.543, M.546, S.589, I.594 Ligands: Y01.29 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.531, C:A.539, C:I.542, C:A.543 Y01.32: 11 residues within 4Å: Chain A: L.529, I.536, I.601, L.605 Chain D: K.698, F.699, N.702, I.703, V.706 Ligands: Y01.6, POV.7 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:L.529, A:I.536, A:I.601, A:L.605, D:F.699, D:I.703, D:V.706 Hydrogen bonds: D:N.702 Y01.35: 17 residues within 4Å: Chain D: W.391, Y.392, M.403, K.406, F.407, V.410, F.440, F.443, A.447, T.451, L.454, V.458, F.607, I.613, A.616, N.617 Ligands: POV.18 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.407, D:F.407, D:V.410, D:V.410, D:F.443, D:A.447, D:L.454, D:V.458, D:F.607, D:I.613, D:A.616 Salt bridges: D:K.406 Y01.38: 8 residues within 4Å: Chain B: F.699 Chain D: M.528, G.532, A.535, A.539, I.594 Ligands: Y01.21, Y01.40 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.535, D:A.539 Y01.40: 8 residues within 4Å: Chain D: F.531, A.539, I.542, A.543, M.546, S.589, I.594 Ligands: Y01.38 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.531, D:A.539, D:I.542, D:A.543

4 x HOR: 4-[[(1R,2R)-2-[(3R)-3-azanylpiperidin-1-yl]-2,3-dihydro-1H-inden-1-yl]oxy]-3-chloranyl-benzenecarbonitrile(Non-covalent)

HOR.4: 12 residues within 4Å: Chain A: K.442, H.446, E.509, E.512, N.527, D.530, R.609, Y.612, I.613, S.752, Y.753, R.758 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.446, A:E.512, A:Y.612, A:Y.612, A:I.613 Hydrogen bonds: A:N.527, A:R.609 Salt bridges: A:D.530 pi-Stacking: A:H.446, A:Y.753 HOR.15: 12 residues within 4Å: Chain B: K.442, H.446, E.509, E.512, N.527, D.530, R.609, Y.612, I.613, S.752, Y.753, R.758 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.446, B:E.512, B:Y.612, B:Y.612, B:I.613 Hydrogen bonds: B:N.527, B:R.609 Salt bridges: B:D.530 pi-Stacking: B:H.446, B:Y.753 HOR.27: 12 residues within 4Å: Chain C: K.442, H.446, E.509, E.512, N.527, D.530, R.609, Y.612, I.613, S.752, Y.753, R.758 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:H.446, C:E.512, C:Y.612, C:Y.612, C:I.613 Hydrogen bonds: C:N.527, C:R.609 Salt bridges: C:D.530 pi-Stacking: C:H.446, C:Y.753 HOR.36: 12 residues within 4Å: Chain D: K.442, H.446, E.509, E.512, N.527, D.530, R.609, Y.612, I.613, S.752, Y.753, R.758 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:H.446, D:E.512, D:Y.612, D:Y.612, D:I.613 Hydrogen bonds: D:N.527, D:R.609 Salt bridges: D:D.530 pi-Stacking: D:H.446, D:Y.753

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

POV.7: 12 residues within 4Å: Chain A: F.641, I.642, F.645, M.649, V.671, E.672, F.675 Chain C: F.465 Chain D: N.702 Ligands: 98R.9, Y01.26, Y01.32 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.641, A:I.642, A:F.645, A:F.645, A:F.675, A:F.675, C:F.465 Salt bridges: A:E.672 POV.18: 12 residues within 4Å: Chain B: F.641, I.642, F.645, M.649, V.671, E.672, F.675 Chain C: N.702 Chain D: F.465 Ligands: 98R.20, Y01.23, Y01.35 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:F.641, B:I.642, B:F.645, B:F.645, B:F.675, B:F.675, D:F.465 Salt bridges: B:E.672 POV.30: 12 residues within 4Å: Chain A: N.702 Chain B: F.465 Chain C: F.641, I.642, F.645, M.649, V.671, E.672, F.675 Ligands: Y01.10, 98R.11, Y01.14 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.641, C:I.642, C:F.645, C:F.645, C:F.675, C:F.675, B:F.465 Salt bridges: C:E.672 POV.39: 12 residues within 4Å: Chain A: F.465 Chain B: N.702 Chain D: F.641, I.642, F.645, M.649, V.671, E.672, F.675 Ligands: Y01.3, Y01.21, 98R.22 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: A:F.465, D:F.641, D:I.642, D:F.645, D:F.645, D:F.675, D:F.675 Salt bridges: D:E.672

4 x 98R: [(2S)-2-[(E)-octadec-10-enoyl]oxy-3-oxidanyl-propyl] octadec-10-enoate(Non-covalent)

98R.9: 11 residues within 4Å: Chain A: E.672, F.675, F.679, W.680 Chain D: N.702, Y.705, V.706, V.713, T.714, I.717 Ligands: POV.7 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:F.675, A:F.675, A:F.679, A:F.679, D:V.713, D:V.713, D:T.714, D:I.717 Hydrogen bonds: D:N.702 98R.11: 11 residues within 4Å: Chain A: N.702, Y.705, V.706, V.713, T.714, I.717 Chain C: E.672, F.675, F.679, W.680 Ligands: POV.30 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:V.713, A:V.713, A:T.714, A:I.717, C:F.675, C:F.675, C:F.679, C:F.679 Hydrogen bonds: A:N.702 98R.20: 11 residues within 4Å: Chain B: E.672, F.675, F.679, W.680 Chain C: N.702, Y.705, V.706, V.713, T.714, I.717 Ligands: POV.18 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:F.675, B:F.675, B:F.679, B:F.679, C:V.713, C:V.713, C:T.714, C:I.717 Hydrogen bonds: C:N.702 98R.22: 11 residues within 4Å: Chain B: N.702, Y.705, V.706, V.713, T.714, I.717 Chain D: E.672, F.675, F.679, W.680 Ligands: POV.39 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:V.713, B:V.713, B:T.714, B:I.717, D:F.675, D:F.675, D:F.679, D:F.679 Hydrogen bonds: B:N.702

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, W. et al., Structural mechanism of human TRPC3 and TRPC6 channel regulation by their intracellular calcium-binding sites. Neuron (2022)

Release Date

2022-02-02

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

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