SMTL ID : 7lqz.1

Structure of squirrel TRPV1 in complex with RTX

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

POV.1: 9 residues within 4Å: Chain A: L.523, F.524, S.542 Chain B: F.657, A.659, V.660, I.663 Ligands: 6EU.2, POV.11 Ligand excluded by PLIP POV.3: 14 residues within 4Å: Chain A: N.439, V.442, Y.443, L.445, V.449, G.486, Y.489, F.490, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.7 Ligand excluded by PLIP POV.4: 10 residues within 4Å: Chain A: V.510, L.576, R.577, C.580, R.581, F.584, L.587 Chain D: Q.563 Ligands: POV.29, POV.31 Ligand excluded by PLIP POV.5: 10 residues within 4Å: Chain A: F.450, V.477, T.478, E.480, S.483, M.525, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP POV.6: 15 residues within 4Å: Chain A: T.451, T.452, Y.455, Y.456 Chain B: M.583, F.584, L.587, F.591, L.632, Y.633, F.640 Chain C: L.666 Ligands: POV.7, POV.8, POV.15 Ligand excluded by PLIP POV.7: 13 residues within 4Å: Chain A: T.452, Y.455, Y.456, G.472, F.475, T.478 Chain B: V.598, T.599, I.601, E.602, N.630 Ligands: POV.3, POV.6 Ligand excluded by PLIP POV.8: 12 residues within 4Å: Chain A: Y.437, F.440, F.441, C.444, L.445, M.554, F.561, Q.562, Q.563, M.564 Ligands: POV.6, POV.15 Ligand excluded by PLIP POV.9: 4 residues within 4Å: Chain A: K.658, L.666 Ligands: POV.33, 6EU.34 Ligand excluded by PLIP POV.11: 5 residues within 4Å: Chain A: Y.633 Chain B: K.658, L.666 Ligands: POV.1, 6EU.2 Ligand excluded by PLIP POV.12: 9 residues within 4Å: Chain B: L.523, F.524, S.542 Chain C: F.657, A.659, V.660, I.663 Ligands: 6EU.13, POV.20 Ligand excluded by PLIP POV.14: 14 residues within 4Å: Chain B: N.439, V.442, Y.443, L.445, V.449, G.486, Y.489, F.490, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.18 Ligand excluded by PLIP POV.15: 10 residues within 4Å: Chain A: Q.563 Chain B: V.510, L.576, R.577, C.580, R.581, F.584, L.587 Ligands: POV.6, POV.8 Ligand excluded by PLIP POV.16: 10 residues within 4Å: Chain B: F.450, V.477, T.478, E.480, S.483, M.525, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP POV.17: 14 residues within 4Å: Chain B: T.451, T.452, Y.455, Y.456 Chain C: M.583, F.584, L.587, F.591, L.632, Y.633 Chain D: L.666 Ligands: POV.18, POV.19, POV.24 Ligand excluded by PLIP POV.18: 15 residues within 4Å: Chain B: T.452, Y.455, Y.456, R.457, G.472, F.475, R.476, T.478 Chain C: V.598, T.599, I.601, E.602, N.630 Ligands: POV.14, POV.17 Ligand excluded by PLIP POV.19: 12 residues within 4Å: Chain B: Y.437, F.440, F.441, C.444, L.445, M.554, F.561, Q.562, Q.563, M.564 Ligands: POV.17, POV.24 Ligand excluded by PLIP POV.20: 5 residues within 4Å: Chain B: Y.633 Chain C: K.658, L.666 Ligands: POV.12, 6EU.13 Ligand excluded by PLIP POV.21: 9 residues within 4Å: Chain C: L.523, F.524, S.542 Chain D: F.657, A.659, V.660, I.663 Ligands: 6EU.22, POV.32 Ligand excluded by PLIP POV.23: 14 residues within 4Å: Chain C: N.439, V.442, Y.443, L.445, V.449, G.486, Y.489, F.490, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.27 Ligand excluded by PLIP POV.24: 9 residues within 4Å: Chain B: Q.563 Chain C: V.510, L.576, R.577, C.580, R.581, L.587 Ligands: POV.17, POV.19 Ligand excluded by PLIP POV.25: 10 residues within 4Å: Chain C: F.450, V.477, T.478, E.480, S.483, M.525, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP POV.26: 15 residues within 4Å: Chain A: L.666 Chain C: T.451, T.452, Y.455, Y.456 Chain D: M.583, F.584, L.587, F.591, L.632, Y.633, F.640 Ligands: POV.27, POV.28, POV.36 Ligand excluded by PLIP POV.27: 13 residues within 4Å: Chain C: T.452, Y.455, Y.456, G.472, F.475, T.478 Chain D: V.598, T.599, I.601, E.602, N.630 Ligands: POV.23, POV.26 Ligand excluded by PLIP POV.28: 12 residues within 4Å: Chain C: Y.437, F.440, F.441, C.444, L.445, M.554, F.561, Q.562, Q.563, M.564 Ligands: POV.26, POV.36 Ligand excluded by PLIP POV.29: 16 residues within 4Å: Chain A: M.583, F.584, L.587, F.591, L.632, Y.633, C.636, F.640 Chain B: L.666 Chain D: T.451, T.452, Y.455, Y.456 Ligands: POV.4, POV.30, POV.31 Ligand excluded by PLIP POV.30: 16 residues within 4Å: Chain A: V.598, T.599, I.601, E.602, N.630 Chain D: T.452, Y.455, Y.456, R.457, G.472, F.475, R.476, T.478, G.479 Ligands: POV.29, POV.35 Ligand excluded by PLIP POV.31: 12 residues within 4Å: Chain D: Y.437, F.440, F.441, C.444, L.445, M.554, F.561, Q.562, Q.563, M.564 Ligands: POV.4, POV.29 Ligand excluded by PLIP POV.32: 4 residues within 4Å: Chain D: K.658, L.666 Ligands: POV.21, 6EU.22 Ligand excluded by PLIP POV.33: 9 residues within 4Å: Chain A: F.657, A.659, V.660, I.663 Chain D: L.523, F.524, S.542 Ligands: POV.9, 6EU.34 Ligand excluded by PLIP POV.35: 14 residues within 4Å: Chain D: N.439, V.442, Y.443, L.445, V.449, G.486, Y.489, F.490, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.30 Ligand excluded by PLIP POV.36: 11 residues within 4Å: Chain C: Q.563, M.564 Chain D: V.510, L.576, R.577, C.580, R.581, F.584, L.587 Ligands: POV.26, POV.28 Ligand excluded by PLIP POV.37: 10 residues within 4Å: Chain D: F.450, V.477, T.478, E.480, S.483, M.525, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP

4 x 6EU: resiniferatoxin(Non-covalent)

6EU.2: 21 residues within 4Å: Chain A: Y.513, S.514, M.516, L.517, F.518, A.548, M.549, T.552, N.553, Y.556, R.559, A.568, I.571, I.575, L.579 Chain B: F.593, A.667, I.670, L.671 Ligands: POV.1, POV.11 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.517, A:L.517, A:I.575, A:L.579, B:F.593, B:I.670, B:L.671 Hydrogen bonds: A:R.559 6EU.13: 22 residues within 4Å: Chain B: Y.513, S.514, M.516, L.517, F.518, A.548, M.549, T.552, N.553, L.555, Y.556, R.559, A.568, I.571, I.575, L.579 Chain C: F.593, A.667, I.670, L.671 Ligands: POV.12, POV.20 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.517, B:L.517, B:I.575, B:L.579, C:F.593, C:F.593, C:L.671 Hydrogen bonds: B:R.559 6EU.22: 21 residues within 4Å: Chain C: Y.513, S.514, M.516, L.517, F.518, A.548, M.549, T.552, N.553, Y.556, R.559, A.568, I.571, I.575, L.579 Chain D: F.593, A.667, I.670, L.671 Ligands: POV.21, POV.32 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.517, C:L.517, C:I.575, C:L.579, D:F.593, D:I.670, D:L.671 Hydrogen bonds: C:R.559 6EU.34: 21 residues within 4Å: Chain A: F.593, A.667, I.670, L.671 Chain D: Y.513, S.514, M.516, L.517, F.518, A.548, M.549, T.552, N.553, Y.556, R.559, A.568, I.571, I.575, L.579 Ligands: POV.9, POV.33 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.517, D:L.517, D:I.575, D:L.579, A:F.593, A:I.670, A:L.671 Hydrogen bonds: D:R.559

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

NA.10: 4 residues within 4Å: Chain A: G.645 Chain B: G.645 Chain C: G.645 Chain D: G.645 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.645

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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