SMTL ID : 9bku.1

Cryo-EM structure of TRPV3 K169A in nanodiscs incubated with NASPM

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

36 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.1: 7 residues within 4Å: Chain A: S.444, K.500, E.501, H.523, F.526, Y.564, Y.565 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.500, A:F.526, A:Y.564 6OU.2: 10 residues within 4Å: Chain A: L.591, Y.594, S.626, D.627, V.629, L.630, F.633 Chain B: L.655 Ligands: 6OU.4, 6OU.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.591, A:Y.594, A:F.633, A:F.633 Hydrogen bonds: A:S.626 6OU.3: 4 residues within 4Å: Chain A: L.553, L.557 Chain B: F.656, L.664 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.553, A:L.557, B:F.656, B:L.664 6OU.4: 7 residues within 4Å: Chain A: I.595, F.625, S.626, V.629 Ligands: 6OU.2, 6OU.11, 6OU.28 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.595, A:F.625, A:V.629 6OU.5: 5 residues within 4Å: Chain A: L.584, L.588, K.589, F.592, I.595 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.589, A:F.592, A:I.595 6OU.6: 7 residues within 4Å: Chain A: K.438, F.441, F.442, F.445, Y.565, G.568, F.569 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.441, A:F.442, A:F.442, A:F.569, A:F.569 6OU.7: 9 residues within 4Å: Chain A: T.456, L.457, Y.460, W.559 Chain B: L.599, V.603, S.624, F.625 Ligands: 6OU.15 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.599, B:L.599, B:V.603, A:T.456, A:W.559, A:W.559 6OU.8: 7 residues within 4Å: Chain A: Y.650, I.652, L.653, F.656 Chain D: L.532, A.549, L.553 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.532, D:A.549, D:L.553, A:L.653, A:F.656 6OU.9: 7 residues within 4Å: Chain A: L.655, F.656, I.659, T.660, I.663 Ligands: 6OU.32, 6OU.34 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.655, A:F.656, A:I.659, A:I.663 6OU.10: 7 residues within 4Å: Chain A: L.532, A.549, L.553 Chain B: Y.650, I.652, L.653, F.656 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.532, A:A.549, A:L.553, B:L.653, B:F.656 6OU.11: 7 residues within 4Å: Chain B: L.655, F.656, I.659, T.660, I.663 Ligands: 6OU.2, 6OU.4 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.655, B:F.656, B:I.659, B:I.663 6OU.12: 7 residues within 4Å: Chain B: S.444, K.500, E.501, H.523, F.526, Y.564, Y.565 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.500, B:F.526, B:Y.564 6OU.13: 10 residues within 4Å: Chain B: L.591, Y.594, S.626, D.627, V.629, L.630, F.633 Chain C: L.655 Ligands: 6OU.15, 6OU.20 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.591, B:Y.594, B:F.633, B:F.633 Hydrogen bonds: B:S.626 6OU.14: 4 residues within 4Å: Chain B: L.553, L.557 Chain C: F.656, L.664 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.656, C:L.664, B:L.553, B:L.557 6OU.15: 7 residues within 4Å: Chain B: I.595, F.625, S.626, V.629 Ligands: 6OU.7, 6OU.13, 6OU.20 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.595, B:F.625, B:V.629 6OU.16: 5 residues within 4Å: Chain B: L.584, L.588, K.589, F.592, I.595 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.589, B:F.592, B:I.595 6OU.17: 7 residues within 4Å: Chain B: K.438, F.441, F.442, F.445, Y.565, G.568, F.569 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.441, B:F.442, B:F.442, B:F.569, B:F.569 6OU.18: 9 residues within 4Å: Chain B: T.456, L.457, Y.460, W.559 Chain C: L.599, V.603, S.624, F.625 Ligands: 6OU.24 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:T.456, B:W.559, B:W.559, C:L.599, C:L.599, C:V.603 6OU.19: 7 residues within 4Å: Chain B: L.532, A.549, L.553 Chain C: Y.650, I.652, L.653, F.656 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.653, C:F.656, B:L.532, B:A.549, B:L.553 6OU.20: 7 residues within 4Å: Chain C: L.655, F.656, I.659, T.660, I.663 Ligands: 6OU.13, 6OU.15 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.655, C:F.656, C:I.659, C:I.663 6OU.21: 7 residues within 4Å: Chain C: S.444, K.500, E.501, H.523, F.526, Y.564, Y.565 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.500, C:F.526, C:Y.564 6OU.22: 10 residues within 4Å: Chain C: L.591, Y.594, S.626, D.627, V.629, L.630, F.633 Chain D: L.655 Ligands: 6OU.24, 6OU.30 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.591, C:Y.594, C:F.633, C:F.633 Hydrogen bonds: C:S.626 6OU.23: 4 residues within 4Å: Chain C: L.553, L.557 Chain D: F.656, L.664 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.553, C:L.557, D:F.656, D:L.664 6OU.24: 7 residues within 4Å: Chain C: I.595, F.625, S.626, V.629 Ligands: 6OU.18, 6OU.22, 6OU.30 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.595, C:F.625, C:V.629 6OU.25: 5 residues within 4Å: Chain C: L.584, L.588, K.589, F.592, I.595 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.589, C:F.592, C:I.595 6OU.26: 7 residues within 4Å: Chain C: K.438, F.441, F.442, F.445, Y.565, G.568, F.569 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.441, C:F.442, C:F.442, C:F.569, C:F.569 6OU.27: 9 residues within 4Å: Chain C: T.456, L.457, Y.460, W.559 Chain D: L.599, V.603, S.624, F.625 Ligands: 6OU.34 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.599, D:L.599, D:V.603, C:T.456, C:W.559, C:W.559 6OU.28: 9 residues within 4Å: Chain A: L.599, V.603, S.624, F.625 Chain D: T.456, L.457, Y.460, W.559 Ligands: 6OU.4 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:L.599, A:L.599, A:V.603, D:T.456, D:W.559, D:W.559 6OU.29: 7 residues within 4Å: Chain C: L.532, A.549, L.553 Chain D: Y.650, I.652, L.653, F.656 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.532, C:A.549, C:L.553, D:L.653, D:F.656 6OU.30: 7 residues within 4Å: Chain D: L.655, F.656, I.659, T.660, I.663 Ligands: 6OU.22, 6OU.24 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.655, D:F.656, D:I.659, D:I.663 6OU.31: 7 residues within 4Å: Chain D: S.444, K.500, E.501, H.523, F.526, Y.564, Y.565 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:K.500, D:F.526, D:Y.564 6OU.32: 10 residues within 4Å: Chain A: L.655 Chain D: L.591, Y.594, S.626, D.627, V.629, L.630, F.633 Ligands: 6OU.9, 6OU.34 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.591, D:Y.594, D:F.633, D:F.633 Hydrogen bonds: D:S.626 6OU.33: 4 residues within 4Å: Chain A: F.656, L.664 Chain D: L.553, L.557 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.553, D:L.557, A:F.656, A:L.664 6OU.34: 7 residues within 4Å: Chain D: I.595, F.625, S.626, V.629 Ligands: 6OU.9, 6OU.27, 6OU.32 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.595, D:F.625, D:V.629 6OU.35: 5 residues within 4Å: Chain D: L.584, L.588, K.589, F.592, I.595 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:K.589, D:F.592, D:I.595 6OU.36: 7 residues within 4Å: Chain D: K.438, F.441, F.442, F.445, Y.565, G.568, F.569 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.441, D:F.442, D:F.442, D:F.569, D:F.569

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Molecular basis of TRPV3 channel blockade by intracellular polyamines. Commun Biol (2025)

Release Date

2025-05-21

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