SMTL ID : 8gka.1

Human TRPV3 tetramer structure, closed conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: G.638 Chain B: G.638 Chain C: G.638 Chain D: G.638 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.638

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

POV.2: 24 residues within 4Å: Chain A: I.583, F.590, L.591, Y.594, L.598, S.626, V.629, F.633, T.636, L.670 Chain D: I.644, Q.645, P.651, I.652, L.655, F.656, I.659, T.660, I.663, V.667 Ligands: POV.3, POV.6, POV.10, POV.28 Ligand excluded by PLIP POV.3: 15 residues within 4Å: Chain A: F.592, I.595, V.596, L.599, V.603, S.624, F.625, S.626 Chain B: I.453, Y.460, Y.461, W.559 Ligands: POV.2, POV.10, POV.12 Ligand excluded by PLIP POV.4: 16 residues within 4Å: Chain A: K.435, F.436, H.439, M.440, S.444, W.493, C.496, V.499, K.500, E.501, F.522, F.526, Y.564, Y.565, F.703, M.706 Ligand excluded by PLIP POV.5: 10 residues within 4Å: Chain A: Q.514, L.517, L.584, H.585, L.588, K.589, F.592 Chain B: S.571, M.572 Ligands: POV.13 Ligand excluded by PLIP POV.6: 23 residues within 4Å: Chain A: L.517, S.518, D.519, A.520, W.521, F.522, L.553, A.556, L.557, A.560, L.563, R.567, S.576, V.577, I.579, Q.580, L.584, Q.695, R.698 Chain D: F.601, L.664 Ligands: POV.2, POV.28 Ligand excluded by PLIP POV.7: 11 residues within 4Å: Chain A: K.649, Y.650, P.651, I.652, L.653, F.656 Chain B: E.546, A.549, C.550, L.553 Ligands: POV.17 Ligand excluded by PLIP POV.8: 16 residues within 4Å: Chain A: I.453, Y.460, Y.461, W.559 Chain D: F.592, I.595, V.596, L.599, V.603, S.624, F.625, S.626 Ligands: POV.9, POV.27, POV.31, POV.34 Ligand excluded by PLIP POV.9: 14 residues within 4Å: Chain A: W.433, K.438, H.439, F.441, F.442, F.445, F.449, M.562, Y.565, T.566, G.568, F.569 Chain D: F.592 Ligands: POV.8 Ligand excluded by PLIP POV.10: 8 residues within 4Å: Chain A: I.595, L.599, F.625, S.626 Chain B: I.453, Y.461 Ligands: POV.2, POV.3 Ligand excluded by PLIP POV.11: 21 residues within 4Å: Chain A: I.644, I.652, L.655, F.656, I.659, T.660, I.663, F.666, V.667 Chain B: L.591, Y.594, L.598, S.626, V.629, L.630, F.633, T.636, L.670 Ligands: POV.14, POV.16, POV.20 Ligand excluded by PLIP POV.12: 17 residues within 4Å: Chain A: F.592, V.596 Chain B: W.433, K.438, H.439, F.441, F.442, F.445, F.449, M.562, Y.565, T.566, R.567, G.568, F.569 Ligands: POV.3, POV.13 Ligand excluded by PLIP POV.13: 9 residues within 4Å: Chain A: L.513, F.592 Chain B: F.569, Q.570, S.571, M.572, W.692 Ligands: POV.5, POV.12 Ligand excluded by PLIP POV.14: 14 residues within 4Å: Chain B: I.595, L.599, G.600, V.603, S.624, F.625, S.626 Chain C: T.456, Y.460, Y.461, W.559 Ligands: POV.11, POV.16, POV.20 Ligand excluded by PLIP POV.15: 15 residues within 4Å: Chain B: K.435, H.439, M.440, L.443, S.444, W.493, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, F.703, M.706 Ligand excluded by PLIP POV.16: 16 residues within 4Å: Chain B: L.513, Q.514, L.517, L.584, H.585, L.588, K.589, L.591, F.592, I.595 Chain C: Q.570, S.571, M.572 Ligands: POV.11, POV.14, POV.20 Ligand excluded by PLIP POV.17: 23 residues within 4Å: Chain A: F.597, T.660, L.664 Chain B: L.517, S.518, D.519, A.520, W.521, F.522, L.553, A.556, L.557, A.560, L.563, R.567, S.576, V.577, I.579, Q.580, I.583, L.584, Q.695 Ligands: POV.7 Ligand excluded by PLIP POV.18: 13 residues within 4Å: Chain B: K.649, Y.650, P.651, I.652, L.653, F.656 Chain C: I.528, L.532, A.549, C.550, L.553 Ligands: POV.19, POV.25 Ligand excluded by PLIP POV.19: 22 residues within 4Å: Chain B: I.644, I.652, L.655, F.656, I.659, T.660, I.663, F.666, V.667 Chain C: I.583, F.590, L.591, Y.594, L.598, S.626, V.629, F.633, T.636, L.670 Ligands: POV.18, POV.22, POV.33 Ligand excluded by PLIP POV.20: 7 residues within 4Å: Chain B: L.599, F.625 Chain C: L.457, Y.461 Ligands: POV.11, POV.14, POV.16 Ligand excluded by PLIP POV.21: 13 residues within 4Å: Chain B: F.592, V.596 Chain C: W.433, K.438, H.439, F.441, F.442, F.445, F.449, M.562, Y.565, G.568, F.569 Ligand excluded by PLIP POV.22: 14 residues within 4Å: Chain C: V.596, L.599, V.603, S.624, F.625, S.626 Chain D: I.453, T.456, Y.460, Y.461, W.559 Ligands: POV.19, POV.29, POV.33 Ligand excluded by PLIP POV.23: 15 residues within 4Å: Chain C: K.435, H.439, M.440, L.443, S.444, W.493, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, F.703, M.706 Ligand excluded by PLIP POV.24: 11 residues within 4Å: Chain C: L.513, Q.514, L.517, L.584, H.585, L.588, K.589, F.592, I.595 Chain D: S.571, M.572 Ligand excluded by PLIP POV.25: 24 residues within 4Å: Chain B: F.597, T.660, L.664 Chain C: L.517, S.518, D.519, A.520, W.521, F.522, I.528, L.553, A.556, L.557, A.560, L.563, R.567, S.576, V.577, I.579, Q.580, I.583, L.584, Q.695 Ligands: POV.18 Ligand excluded by PLIP POV.26: 11 residues within 4Å: Chain C: K.649, Y.650, P.651, I.652, L.653, F.656 Chain D: A.549, C.550, L.553 Ligands: POV.32, POV.34 Ligand excluded by PLIP POV.27: 8 residues within 4Å: Chain A: F.449, Y.461 Chain D: I.595, L.599, F.625, S.626 Ligands: POV.8, POV.34 Ligand excluded by PLIP POV.28: 12 residues within 4Å: Chain A: E.546, A.549, C.550, L.553 Chain D: K.649, Y.650, P.651, I.652, L.653, F.656 Ligands: POV.2, POV.6 Ligand excluded by PLIP POV.29: 13 residues within 4Å: Chain C: F.592, V.596 Chain D: W.433, K.438, H.439, F.441, F.442, F.445, M.562, Y.565, G.568, F.569 Ligands: POV.22 Ligand excluded by PLIP POV.30: 18 residues within 4Å: Chain D: K.435, F.436, H.439, M.440, L.443, S.444, W.493, C.496, V.499, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, F.703, M.706 Ligand excluded by PLIP POV.31: 15 residues within 4Å: Chain A: Q.570, S.571, M.572 Chain D: L.513, Q.514, L.517, L.584, H.585, L.588, K.589, F.592, I.595 Ligands: POV.8, POV.32, POV.34 Ligand excluded by PLIP POV.32: 24 residues within 4Å: Chain C: T.660, L.664 Chain D: L.517, S.518, D.519, A.520, W.521, F.522, I.528, L.557, A.560, L.563, R.567, S.576, V.577, I.579, Q.580, I.583, L.584, L.588, Q.695, R.698 Ligands: POV.26, POV.31 Ligand excluded by PLIP POV.33: 6 residues within 4Å: Chain C: F.625 Chain D: F.449, L.457, Y.461 Ligands: POV.19, POV.22 Ligand excluded by PLIP POV.34: 22 residues within 4Å: Chain C: I.644, I.652, L.655, F.656, I.659, T.660, I.663, F.666, V.667 Chain D: L.591, Y.594, L.598, S.626, V.629, L.630, F.633, T.636, L.670 Ligands: POV.8, POV.26, POV.27, POV.31 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lansky, S. et al., A pentameric TRPV3 channel with a dilated pore. Nature (2023)

Release Date

2023-09-06

Peptides

Transient receptor potential cation channel subfamily V member 3: 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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Transient receptor potential cation channel subfamily V member 3

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