SMTL ID : 7e4t.1

Human TRPC5 apo state structure at 3 angstrom

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 15 residues within 4Å: Chain A: D.433, W.434, W.435, M.438, I.484, I.487, L.491, I.494, Q.507, G.511, K.645 Chain D: T.603, T.607 Ligands: POV.2, YZY.6 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain A Hydrophobic interactions: D:T.603, D:T.607, A:W.435, A:M.438, A:I.484, A:I.484, A:I.487, A:I.494 Hydrogen bonds: A:Q.507 Salt bridges: A:K.645 PTY.7: 15 residues within 4Å: Chain A: T.603, T.607 Chain B: D.433, W.434, W.435, M.438, I.484, I.487, L.491, I.494, Q.507, G.511, K.645 Ligands: POV.8, YZY.12 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.435, B:M.438, B:I.484, B:I.484, B:I.487, B:I.494, A:T.603, A:T.607 Hydrogen bonds: B:Q.507 Salt bridges: B:K.645 PTY.13: 15 residues within 4Å: Chain B: T.603, T.607 Chain C: D.433, W.434, W.435, M.438, I.484, I.487, L.491, I.494, Q.507, G.511, K.645 Ligands: POV.14, YZY.18 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.435, C:M.438, C:I.484, C:I.484, C:I.487, C:I.494, B:T.603, B:T.607 Hydrogen bonds: C:Q.507 Salt bridges: C:K.645 PTY.19: 15 residues within 4Å: Chain C: T.603, T.607 Chain D: D.433, W.434, W.435, M.438, I.484, I.487, L.491, I.494, Q.507, G.511, K.645 Ligands: POV.20, YZY.24 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.435, D:M.438, D:I.484, D:I.484, D:I.487, D:I.494, C:T.603, C:T.607 Hydrogen bonds: D:Q.507 Salt bridges: D:K.645

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

POV.2: 8 residues within 4Å: Chain A: A.441, S.444, L.445, W.472, I.477, L.481 Chain D: F.596 Ligands: PTY.1 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:F.596, A:L.445 Hydrogen bonds: A:W.472 POV.8: 8 residues within 4Å: Chain A: F.596 Chain B: A.441, S.444, L.445, W.472, I.477, L.481 Ligands: PTY.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.596, B:L.445 Hydrogen bonds: B:W.472 POV.14: 8 residues within 4Å: Chain B: F.596 Chain C: A.441, S.444, L.445, W.472, I.477, L.481 Ligands: PTY.13 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.445, B:F.596 Hydrogen bonds: C:W.472 POV.20: 8 residues within 4Å: Chain C: F.596 Chain D: A.441, S.444, L.445, W.472, I.477, L.481 Ligands: PTY.19 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.445, C:F.596 Hydrogen bonds: D:W.472

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 13 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: F.522, L.526, L.529 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:T.371, A:L.375, A:L.493, A:F.497, A:F.497, D:F.522, D:L.526, D:L.529 Hydrogen bonds: A:A.499, A:N.500 Y01.9: 13 residues within 4Å: Chain A: F.522, L.526, L.529 Chain B: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.371, B:L.375, B:L.493, B:F.497, B:F.497, A:F.522, A:L.526, A:L.529 Hydrogen bonds: B:A.499, B:N.500 Y01.15: 13 residues within 4Å: Chain B: F.522, L.526, L.529 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: 3 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:F.522, B:L.526, B:L.529, C:T.371, C:L.375, C:L.493, C:F.497, C:F.497 Hydrogen bonds: C:A.499, C:N.500 Y01.21: 13 residues within 4Å: Chain C: F.522, L.526, L.529 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: 3 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:F.522, C:L.526, C:L.529, D:T.371, D:L.375, D:L.493, D:F.497, D:F.497 Hydrogen bonds: 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 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.418, A:D.439 CA.11: 5 residues within 4Å: Chain B: E.418, E.421, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.418, B:D.439 CA.17: 5 residues within 4Å: Chain C: E.418, E.421, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.418, C:D.439 CA.23: 5 residues within 4Å: Chain D: E.418, E.421, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.418, D:D.439

4 x YZY: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

YZY.6: 12 residues within 4Å: Chain A: L.521, Y.524, L.528, Q.573, F.576, W.577 Chain D: F.599, V.610, I.611, V.614, V.615 Ligands: PTY.1 11 PLIP interactions: 4 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:V.610, D:I.611, D:V.614, D:V.615, A:L.521, A:Y.524, A:L.528, A:F.576, A:F.576 Hydrogen bonds: A:Q.573, A:W.577 YZY.12: 12 residues within 4Å: Chain A: F.599, V.610, I.611, V.614, V.615 Chain B: L.521, Y.524, L.528, Q.573, F.576, W.577 Ligands: PTY.7 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.521, B:Y.524, B:L.528, B:F.576, B:F.576, A:V.610, A:I.611, A:V.614, A:V.615 Hydrogen bonds: B:Q.573, B:W.577 YZY.18: 12 residues within 4Å: Chain B: F.599, V.610, I.611, V.614, V.615 Chain C: L.521, Y.524, L.528, Q.573, F.576, W.577 Ligands: PTY.13 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:V.610, B:I.611, B:V.614, B:V.615, C:L.521, C:Y.524, C:L.528, C:F.576, C:F.576 Hydrogen bonds: C:Q.573, C:W.577 YZY.24: 12 residues within 4Å: Chain C: F.599, V.610, I.611, V.614, V.615 Chain D: L.521, Y.524, L.528, Q.573, F.576, W.577 Ligands: PTY.19 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.521, D:Y.524, D:L.528, D:F.576, D:F.576, C:V.610, C:I.611, C:V.614, C:V.615 Hydrogen bonds: D:Q.573, D:W.577

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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