SMTL ID : 7lqy.1

Structure of squirrel TRPV1 in apo state

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: 12 residues within 4Å: Chain A: V.520, L.523, E.538, A.541, S.542, F.545 Chain B: F.657, A.659, V.660, I.663 Ligands: POV.2, YBG.3 Ligand excluded by PLIP POV.2: 10 residues within 4Å: Chain A: Y.633 Chain B: K.658, A.659, I.663, L.666, A.667, L.671 Ligands: POV.1, POV.5, POV.30 Ligand excluded by PLIP POV.4: 18 residues within 4Å: Chain A: F.438, N.439, F.441, 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 Ligands: POV.8 Ligand excluded by PLIP POV.5: 15 residues within 4Å: Chain A: Y.513, K.573, I.575, L.576, R.577, C.580, R.581, M.583, F.584, L.587 Chain D: Q.563 Ligands: POV.2, YBG.3, POV.30, POV.32 Ligand excluded by PLIP POV.6: 10 residues within 4Å: Chain A: F.450, L.467, V.477, E.480, S.483, V.484, M.525, Y.532, F.533, M.543 Ligand excluded by PLIP POV.7: 19 residues within 4Å: Chain A: I.448, T.451, T.452, Y.455, Y.456 Chain B: L.587, V.588, L.590, F.591, S.631, L.632, Y.633, C.636, F.640 Chain C: L.666 Ligands: POV.8, POV.9, POV.13, POV.16 Ligand excluded by PLIP POV.8: 15 residues within 4Å: Chain A: I.448, V.449, T.452, A.453, Y.455, Y.456, G.472, F.475, R.476, T.478, G.479 Chain B: N.630 Ligands: POV.4, POV.7, POV.9 Ligand excluded by PLIP POV.9: 15 residues within 4Å: Chain A: K.433, F.440, F.441, C.444, L.445, I.448, W.551, G.560, F.561, Q.562, M.564 Chain B: F.584 Ligands: POV.7, POV.8, POV.16 Ligand excluded by PLIP POV.12: 12 residues within 4Å: Chain B: V.520, L.523, E.538, A.541, S.542, F.545 Chain C: F.657, A.659, V.660, I.663 Ligands: POV.13, YBG.14 Ligand excluded by PLIP POV.13: 10 residues within 4Å: Chain B: Y.633 Chain C: K.658, A.659, I.663, L.666, A.667, L.671 Ligands: POV.7, POV.12, POV.16 Ligand excluded by PLIP POV.15: 18 residues within 4Å: Chain B: F.438, N.439, F.441, 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 Ligands: POV.19 Ligand excluded by PLIP POV.16: 16 residues within 4Å: Chain A: Q.563 Chain B: V.510, Y.513, K.573, I.575, L.576, R.577, C.580, R.581, M.583, F.584, L.587 Ligands: POV.7, POV.9, POV.13, YBG.14 Ligand excluded by PLIP POV.17: 10 residues within 4Å: Chain B: F.450, L.467, V.477, E.480, S.483, V.484, M.525, Y.532, F.533, M.543 Ligand excluded by PLIP POV.18: 19 residues within 4Å: Chain B: I.448, T.451, T.452, Y.455, Y.456 Chain C: L.587, V.588, L.590, F.591, S.631, L.632, Y.633, C.636, F.640 Chain D: L.666 Ligands: POV.19, POV.20, POV.22, POV.25 Ligand excluded by PLIP POV.19: 15 residues within 4Å: Chain B: I.448, V.449, T.452, A.453, Y.455, Y.456, G.472, F.475, R.476, T.478, G.479 Chain C: N.630 Ligands: POV.15, POV.18, POV.20 Ligand excluded by PLIP POV.20: 16 residues within 4Å: Chain B: K.433, Y.437, F.440, F.441, C.444, L.445, I.448, W.551, G.560, F.561, Q.562, M.564 Chain C: F.584 Ligands: POV.18, POV.19, POV.25 Ligand excluded by PLIP POV.21: 12 residues within 4Å: Chain C: V.520, L.523, E.538, A.541, S.542, F.545 Chain D: F.657, A.659, V.660, I.663 Ligands: POV.22, YBG.23 Ligand excluded by PLIP POV.22: 10 residues within 4Å: Chain C: Y.633 Chain D: K.658, A.659, I.663, L.666, A.667, L.671 Ligands: POV.18, POV.21, POV.25 Ligand excluded by PLIP POV.24: 18 residues within 4Å: Chain C: F.438, N.439, F.441, 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 Ligands: POV.28 Ligand excluded by PLIP POV.25: 15 residues within 4Å: Chain B: Q.563 Chain C: Y.513, K.573, I.575, L.576, R.577, C.580, R.581, M.583, F.584, L.587 Ligands: POV.18, POV.20, POV.22, YBG.23 Ligand excluded by PLIP POV.26: 10 residues within 4Å: Chain C: F.450, L.467, V.477, E.480, S.483, V.484, M.525, Y.532, F.533, M.543 Ligand excluded by PLIP POV.27: 19 residues within 4Å: Chain A: L.666 Chain C: I.448, T.451, T.452, Y.455, Y.456 Chain D: L.587, V.588, L.590, F.591, S.631, L.632, Y.633, C.636, F.640 Ligands: POV.28, POV.29, POV.34, POV.37 Ligand excluded by PLIP POV.28: 15 residues within 4Å: Chain C: I.448, V.449, T.452, A.453, Y.455, Y.456, G.472, F.475, R.476, T.478, G.479 Chain D: N.630 Ligands: POV.24, POV.27, POV.29 Ligand excluded by PLIP POV.29: 16 residues within 4Å: Chain C: K.433, Y.437, F.440, F.441, C.444, L.445, I.448, W.551, G.560, F.561, Q.562, M.564 Chain D: F.584 Ligands: POV.27, POV.28, POV.37 Ligand excluded by PLIP POV.30: 19 residues within 4Å: Chain A: L.587, V.588, L.590, F.591, S.631, L.632, Y.633, C.636, F.640 Chain B: L.666 Chain D: I.448, T.451, T.452, Y.455, Y.456 Ligands: POV.2, POV.5, POV.31, POV.32 Ligand excluded by PLIP POV.31: 15 residues within 4Å: Chain A: N.630 Chain D: I.448, V.449, T.452, A.453, Y.455, Y.456, G.472, F.475, R.476, T.478, G.479 Ligands: POV.30, POV.32, POV.36 Ligand excluded by PLIP POV.32: 16 residues within 4Å: Chain A: F.584 Chain D: K.433, Y.437, F.440, F.441, C.444, L.445, I.448, W.551, G.560, F.561, Q.562, M.564 Ligands: POV.5, POV.30, POV.31 Ligand excluded by PLIP POV.33: 12 residues within 4Å: Chain A: F.657, A.659, V.660, I.663 Chain D: V.520, L.523, E.538, A.541, S.542, F.545 Ligands: POV.34, YBG.35 Ligand excluded by PLIP POV.34: 10 residues within 4Å: Chain A: K.658, A.659, I.663, L.666, A.667, L.671 Chain D: Y.633 Ligands: POV.27, POV.33, POV.37 Ligand excluded by PLIP POV.36: 18 residues within 4Å: Chain D: F.438, N.439, F.441, 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 Ligands: POV.31 Ligand excluded by PLIP POV.37: 15 residues within 4Å: Chain C: Q.563 Chain D: Y.513, K.573, I.575, L.576, R.577, C.580, R.581, M.583, F.584, L.587 Ligands: POV.27, POV.29, POV.34, YBG.35 Ligand excluded by PLIP POV.38: 9 residues within 4Å: Chain D: F.450, L.467, V.477, E.480, V.484, M.525, Y.532, F.533, M.543 Ligand excluded by PLIP

4 x YBG: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol(Non-covalent)

YBG.3: 27 residues within 4Å: Chain A: R.411, H.412, D.511, S.512, Y.513, S.514, M.516, L.517, F.545, A.548, M.549, T.552, L.555, Y.556, R.559, E.572, I.575, L.576, I.698, L.701, Q.702, I.705 Chain B: F.593, A.667, L.671 Ligands: POV.1, POV.5 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.513, A:Y.513, A:M.516, A:F.545, A:M.549, A:T.552, A:I.575, A:I.575, A:L.576, B:F.593, B:F.593, B:A.667, B:L.671 Hydrogen bonds: A:R.411, A:R.411, A:Y.513, A:S.514, A:K.573, A:Q.702 Salt bridges: A:R.559 YBG.14: 27 residues within 4Å: Chain B: R.411, H.412, D.511, S.512, Y.513, S.514, M.516, L.517, F.545, A.548, M.549, T.552, L.555, Y.556, R.559, E.572, I.575, L.576, I.698, L.701, Q.702, I.705 Chain C: F.593, A.667, L.671 Ligands: POV.12, POV.16 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:Y.513, B:Y.513, B:M.516, B:F.545, B:M.549, B:I.575, B:I.575, B:L.576, C:F.593, C:A.667, C:L.671 Hydrogen bonds: B:R.411, B:R.411, B:Y.513, B:S.514, B:E.572, B:K.573, B:Q.702 Salt bridges: B:R.559 YBG.23: 27 residues within 4Å: Chain C: R.411, H.412, D.511, S.512, Y.513, S.514, M.516, L.517, F.545, A.548, M.549, T.552, L.555, Y.556, R.559, E.572, I.575, L.576, I.698, L.701, Q.702, I.705 Chain D: F.593, A.667, L.671 Ligands: POV.21, POV.25 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.513, C:Y.513, C:M.516, C:F.545, C:I.575, C:I.575, C:L.576, D:F.593, D:A.667, D:L.671 Hydrogen bonds: C:R.411, C:R.411, C:Y.513, C:S.514, C:K.573, C:Q.702 Salt bridges: C:R.559 YBG.35: 27 residues within 4Å: Chain A: F.593, A.667, L.671 Chain D: R.411, H.412, D.511, S.512, Y.513, S.514, M.516, L.517, F.545, A.548, M.549, T.552, L.555, Y.556, R.559, E.572, I.575, L.576, I.698, L.701, Q.702, I.705 Ligands: POV.33, POV.37 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.513, D:Y.513, D:M.516, D:F.545, D:M.549, D:I.575, D:I.575, D:L.576, A:F.593, A:A.667, A:L.671 Hydrogen bonds: D:R.411, D:R.411, D:Y.513, D:S.514, D:K.573, D:Q.702 Salt bridges: D:R.559

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 4 residues within 4Å: Chain A: R.624 Chain B: R.624 Chain C: R.624 Chain D: R.624 Ligand excluded by PLIP

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

NA.11: 8 residues within 4Å: Chain A: G.645, M.646 Chain B: G.645, M.646 Chain C: G.645, M.646 Chain D: G.645, M.646 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.
Show / Hide

Osm-9-like TRP channel 1

Related Entries With Identical Sequence