SMTL ID : 7lr0.1

Structure of squirrel TRPV1 in complex with capsaicin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

POV.1: 17 residues within 4Å: Chain A: V.520, L.523, F.524, G.527, R.536, E.538, A.541, S.542, F.545 Chain B: D.656, F.657, A.659, V.660, I.663 Ligands: POV.2, 4DY.3, POV.5 Ligand excluded by PLIP POV.2: 16 residues within 4Å: Chain A: I.575, L.579, Y.633 Chain B: K.658, A.659, I.662, I.663, L.666, A.667, I.670, L.671 Ligands: POV.1, 4DY.3, POV.5, POV.27, POV.28 Ligand excluded by PLIP POV.4: 18 residues within 4Å: Chain A: F.438, N.439, V.442, Y.443, L.445, Y.446, V.449, L.482, G.486, Y.489, F.490, R.493, S.514, E.515, F.518, Y.556, Y.557, D.709 Ligand excluded by PLIP POV.5: 12 residues within 4Å: Chain A: V.510, Y.513, L.517, V.520, F.524, M.549, I.575, L.576, L.579 Ligands: POV.1, POV.2, 4DY.3 Ligand excluded by PLIP POV.6: 12 residues within 4Å: Chain A: F.450, R.476, V.477, E.480, I.481, V.484, M.525, S.528, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP POV.7: 17 residues within 4Å: Chain A: I.448, T.451, Y.455, Y.456 Chain B: M.583, Y.586, L.587, L.590, F.591, L.632, Y.633, C.636, L.637, F.640 Chain C: L.666, I.670 Ligands: POV.12 Ligand excluded by PLIP POV.8: 17 residues within 4Å: Chain A: K.433, Y.437, F.440, F.441, C.444, L.445, I.448, F.561, Q.562, Q.563, M.564 Chain B: L.579, C.580, M.583, F.584, L.587 Ligands: POV.12 Ligand excluded by PLIP POV.9: 15 residues within 4Å: Chain A: D.656, F.657, A.659, V.660, I.663 Chain D: V.520, L.523, F.524, R.536, E.538, S.542, F.545 Ligands: POV.29, 4DY.30, POV.32 Ligand excluded by PLIP POV.11: 15 residues within 4Å: Chain B: V.520, L.523, F.524, R.536, E.538, S.542, F.545 Chain C: D.656, F.657, A.659, V.660, I.663 Ligands: POV.12, 4DY.13, POV.15 Ligand excluded by PLIP POV.12: 16 residues within 4Å: Chain B: I.575, L.579, Y.633 Chain C: K.658, A.659, I.662, I.663, L.666, A.667, I.670, L.671 Ligands: POV.7, POV.8, POV.11, 4DY.13, POV.15 Ligand excluded by PLIP POV.14: 18 residues within 4Å: Chain B: F.438, N.439, V.442, Y.443, L.445, Y.446, V.449, L.482, G.486, Y.489, F.490, R.493, S.514, E.515, F.518, Y.556, Y.557, D.709 Ligand excluded by PLIP POV.15: 12 residues within 4Å: Chain B: V.510, Y.513, L.517, V.520, F.524, M.549, I.575, L.576, L.579 Ligands: POV.11, POV.12, 4DY.13 Ligand excluded by PLIP POV.16: 12 residues within 4Å: Chain B: F.450, R.476, V.477, E.480, I.481, V.484, M.525, S.528, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP POV.17: 18 residues within 4Å: Chain B: I.448, T.451, Y.455, Y.456 Chain C: M.583, Y.586, L.587, L.590, F.591, S.631, L.632, Y.633, C.636, L.637, F.640 Chain D: L.666, I.670 Ligands: POV.20 Ligand excluded by PLIP POV.18: 17 residues within 4Å: Chain B: K.433, Y.437, F.440, F.441, C.444, L.445, I.448, F.561, Q.562, Q.563, M.564 Chain C: L.579, C.580, M.583, F.584, L.587 Ligands: POV.20 Ligand excluded by PLIP POV.19: 15 residues within 4Å: Chain C: V.520, L.523, F.524, R.536, E.538, S.542, F.545 Chain D: D.656, F.657, A.659, V.660, I.663 Ligands: POV.20, 4DY.21, POV.23 Ligand excluded by PLIP POV.20: 16 residues within 4Å: Chain C: I.575, L.579, Y.633 Chain D: K.658, A.659, I.662, I.663, L.666, A.667, I.670, L.671 Ligands: POV.17, POV.18, POV.19, 4DY.21, POV.23 Ligand excluded by PLIP POV.22: 18 residues within 4Å: Chain C: F.438, N.439, V.442, Y.443, L.445, Y.446, V.449, L.482, G.486, Y.489, F.490, R.493, S.514, E.515, F.518, Y.556, Y.557, D.709 Ligand excluded by PLIP POV.23: 12 residues within 4Å: Chain C: V.510, Y.513, L.517, V.520, F.524, M.549, I.575, L.576, L.579 Ligands: POV.19, POV.20, 4DY.21 Ligand excluded by PLIP POV.24: 12 residues within 4Å: Chain C: F.450, R.476, V.477, E.480, I.481, V.484, M.525, S.528, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP POV.25: 18 residues within 4Å: Chain A: L.666, I.670 Chain C: I.448, T.451, Y.455, Y.456 Chain D: M.583, Y.586, L.587, L.590, F.591, S.631, L.632, Y.633, C.636, L.637, F.640 Ligands: POV.29 Ligand excluded by PLIP POV.26: 17 residues within 4Å: Chain C: K.433, Y.437, F.440, F.441, C.444, L.445, I.448, F.561, Q.562, Q.563, M.564 Chain D: L.579, C.580, M.583, F.584, L.587 Ligands: POV.29 Ligand excluded by PLIP POV.27: 17 residues within 4Å: Chain A: M.583, Y.586, L.587, L.590, F.591, L.632, Y.633, C.636, L.637, F.640 Chain B: L.666, I.670 Chain D: I.448, T.451, Y.455, Y.456 Ligands: POV.2 Ligand excluded by PLIP POV.28: 17 residues within 4Å: Chain A: L.579, C.580, M.583, F.584, L.587 Chain D: K.433, Y.437, F.440, F.441, C.444, L.445, I.448, F.561, Q.562, Q.563, M.564 Ligands: POV.2 Ligand excluded by PLIP POV.29: 16 residues within 4Å: Chain A: K.658, A.659, I.662, I.663, L.666, A.667, I.670, L.671 Chain D: I.575, L.579, Y.633 Ligands: POV.9, POV.25, POV.26, 4DY.30, POV.32 Ligand excluded by PLIP POV.31: 17 residues within 4Å: Chain D: F.438, N.439, V.442, Y.443, L.445, Y.446, V.449, G.486, Y.489, F.490, R.493, S.514, E.515, F.518, Y.556, Y.557, D.709 Ligand excluded by PLIP POV.32: 12 residues within 4Å: Chain D: V.510, Y.513, L.517, V.520, F.524, M.549, I.575, L.576, L.579 Ligands: POV.9, POV.29, 4DY.30 Ligand excluded by PLIP POV.33: 12 residues within 4Å: Chain D: F.450, R.476, V.477, E.480, I.481, V.484, M.525, S.528, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP

4 x 4DY: (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide(Non-covalent)

4DY.3: 25 residues within 4Å: Chain A: Y.513, S.514, L.517, F.518, F.545, A.548, M.549, T.552, N.553, L.555, Y.556, R.559, A.568, I.571, E.572, I.575 Chain B: F.589, F.593, I.663, L.664, A.667, L.671 Ligands: POV.1, POV.2, POV.5 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.545, A:T.552, A:L.555, A:I.571, B:F.593, B:F.593, B:L.664, B:L.671 Hydrogen bonds: A:Y.513 4DY.13: 25 residues within 4Å: Chain B: Y.513, S.514, L.517, F.518, F.545, A.548, M.549, T.552, N.553, L.555, Y.556, R.559, A.568, I.571, E.572, I.575 Chain C: F.589, F.593, I.663, L.664, A.667, L.671 Ligands: POV.11, POV.12, POV.15 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:F.593, C:F.593, C:L.664, C:L.671, B:F.545, B:T.552, B:L.555, B:I.571 Hydrogen bonds: B:Y.513 4DY.21: 25 residues within 4Å: Chain C: Y.513, S.514, L.517, F.518, F.545, A.548, M.549, T.552, N.553, L.555, Y.556, R.559, A.568, I.571, E.572, I.575 Chain D: F.589, F.593, I.663, L.664, A.667, L.671 Ligands: POV.19, POV.20, POV.23 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.593, D:F.593, D:L.664, D:L.671, C:T.552, C:L.555, C:I.571 Hydrogen bonds: C:Y.513 4DY.30: 25 residues within 4Å: Chain A: F.589, F.593, I.663, L.664, A.667, L.671 Chain D: Y.513, S.514, L.517, F.518, F.545, A.548, M.549, T.552, N.553, L.555, Y.556, R.559, A.568, I.571, E.572, I.575 Ligands: POV.9, POV.29, POV.32 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:F.593, A:F.593, A:L.664, A:L.671, D:F.545, D:T.552, D:L.555, D:I.571 Hydrogen bonds: D:Y.513, D:Y.513

1 x NA: SODIUM ION(Non-functional Binders)

NA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nadezhdin, K.D. et al., Extracellular cap domain is an essential component of the TRPV1 gating mechanism. Nat Commun (2021)

Release Date

2021-04-21

Peptides

Osm-9-like TRP channel 1: 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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Osm-9-like TRP channel 1

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