SMTL ID : 7xj0.1

Structure of human TRPV3 in complex with Trpvicin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

6OU.1: 3 residues within 4Å: Chain A: L.553, L.557 Ligands: EQK.7 No protein-ligand interaction detected (PLIP) 6OU.2: 9 residues within 4Å: Chain A: L.591, Y.594, L.598, S.626, L.630, F.633 Chain B: I.644, I.659, V.667 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.591, A:Y.594, A:L.598, A:L.630, A:F.633, A:F.633, A:F.633, B:I.644, B:I.659, B:V.667 6OU.3: 2 residues within 4Å: Chain A: L.599, V.629 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.629 6OU.4: 5 residues within 4Å: Chain A: I.652, L.655, I.659 Ligands: 6OU.14, 6OU.19 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.652, A:I.652, A:L.655, A:I.659, A:I.659 6OU.5: 15 residues within 4Å: Chain A: W.433, K.438, F.441, F.442, F.445, A.560, M.562, L.563, Y.565, T.566, F.569, I.579 Chain B: V.593, F.597 Ligands: EQK.7 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.445, A:A.560, A:M.562, A:L.563, A:F.569, A:I.579, B:V.593, B:F.597, B:F.597 Hydrogen bonds: A:K.438 Salt bridges: A:K.438 6OU.8: 16 residues within 4Å: Chain B: W.433, K.438, F.441, F.442, F.445, W.521, M.562, L.563, Y.565, T.566, G.568, F.569, I.579 Chain D: V.593, F.597 Ligands: EQK.20 10 PLIP interactions: 1 interactions with chain D, 9 interactions with chain B Hydrophobic interactions: D:V.593, B:F.445, B:W.521, B:L.563, B:F.569, B:I.579 Hydrogen bonds: B:K.438, B:K.438, B:K.438 Salt bridges: B:K.438 6OU.9: 4 residues within 4Å: Chain B: L.599, S.626, V.629 Ligands: 6OU.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.599, B:V.629 6OU.10: 11 residues within 4Å: Chain B: L.591, Y.594, L.598, S.626, V.629, L.630, F.633 Chain D: I.659, I.663 Ligands: 6OU.9, 6OU.22 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.591, B:Y.594, B:L.598, B:V.629, B:L.630, B:F.633, B:F.633, B:F.633, D:I.663 6OU.11: 3 residues within 4Å: Chain B: I.652, L.655, F.656 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.652, B:L.655 6OU.12: 5 residues within 4Å: Chain B: A.549, C.550, L.553, L.557 Ligands: EQK.20 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.549, B:L.553, B:L.557 6OU.13: 7 residues within 4Å: Chain C: V.525, L.532, A.549, C.550, L.553, L.557 Ligands: EQK.6 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.525, C:L.532, C:A.549, C:L.553, C:L.553, C:L.557 6OU.14: 10 residues within 4Å: Chain A: I.659, I.663, V.667 Chain C: L.591, Y.594, L.598, S.626, L.630, F.633 Ligands: 6OU.4 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:I.659, A:I.663, A:V.667, C:L.591, C:Y.594, C:L.598, C:L.630, C:L.630, C:F.633, C:F.633 6OU.15: 11 residues within 4Å: Chain C: I.644, L.655, I.659 Chain D: Y.594, L.598, S.626, V.629, L.630, F.633 Ligands: 6OU.16, 6OU.23 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:I.644, C:L.655, C:I.659, C:I.659, D:Y.594, D:L.598, D:V.629, D:L.630, D:F.633, D:F.633, D:F.633 6OU.16: 6 residues within 4Å: Chain C: I.652, L.655, F.656, I.659, I.663 Ligands: 6OU.15 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.652, C:I.652, C:L.655, C:F.656, C:I.659, C:I.659, C:I.663 6OU.17: 16 residues within 4Å: Chain A: V.593, F.597 Chain C: W.433, K.438, F.441, F.442, F.445, A.560, M.562, L.563, Y.565, T.566, G.568, F.569, I.579 Ligands: EQK.6 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.445, C:A.560, C:L.563, C:F.569, C:I.579, A:V.593, A:F.597 Hydrogen bonds: C:K.438, C:K.438 6OU.19: 1 residues within 4Å: Ligands: 6OU.4 No protein-ligand interaction detected (PLIP) 6OU.21: 4 residues within 4Å: Chain D: A.549, L.553, L.557 Ligands: EQK.18 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:A.549, D:L.553, D:L.553, D:L.557 6OU.22: 4 residues within 4Å: Chain D: I.652, L.655, I.659 Ligands: 6OU.10 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.652, D:I.652, D:L.655, D:I.659, D:I.659 6OU.23: 4 residues within 4Å: Chain D: I.595, L.599, S.626 Ligands: 6OU.15 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.595 6OU.24: 13 residues within 4Å: Chain C: F.597 Chain D: K.438, H.439, F.441, F.442, F.445, W.521, M.562, L.563, Y.565, T.566, F.569 Ligands: EQK.18 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.521, D:M.562, D:L.563, D:T.566, D:F.569, C:F.597 Hydrogen bonds: D:F.442 Salt bridges: D:K.438

4 x EQK: N-[5-[2-(2-cyanopropan-2-yl)pyridin-4-yl]-4-(trifluoromethyl)-1,3-thiazol-2-yl]-4,6-dimethoxy-pyrimidine-5-carboxamide(Non-covalent)

EQK.6: 16 residues within 4Å: Chain A: V.596, F.597, G.600, F.601, F.656, T.660, I.663, L.664 Chain C: L.553, A.556, L.557, W.559, A.560, I.583 Ligands: 6OU.13, 6OU.17 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:W.559, A:F.597, A:F.601, A:F.656, A:T.660, A:I.663, A:L.664 Hydrogen bonds: C:A.556, C:A.560 Halogen bonds: C:L.553 EQK.7: 16 residues within 4Å: Chain A: L.553, A.556, L.557, W.559, A.560, I.583 Chain B: V.596, F.597, G.600, F.601, F.656, T.660, I.663, L.664 Ligands: 6OU.1, 6OU.5 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:W.559, B:F.597, B:F.601, B:F.656, B:T.660, B:I.663, B:L.664 Hydrogen bonds: A:A.556, A:A.560 Halogen bonds: A:L.553 EQK.18: 17 residues within 4Å: Chain C: V.596, F.597, G.600, F.601, A.604, F.656, T.660, I.663, L.664 Chain D: L.553, A.556, L.557, W.559, A.560, I.583 Ligands: 6OU.21, 6OU.24 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.601, C:F.656, C:T.660, C:I.663, C:L.664, D:W.559 Hydrogen bonds: D:A.556, D:A.560 Halogen bonds: D:L.553 EQK.20: 16 residues within 4Å: Chain B: L.553, A.556, L.557, W.559, A.560, I.583 Chain D: V.596, F.597, G.600, F.601, F.656, T.660, I.663, L.664 Ligands: 6OU.8, 6OU.12 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:W.559, D:F.656, D:T.660, D:I.663, D:L.664 Hydrogen bonds: B:A.560 Halogen bonds: B:L.553

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, J. et al., Structural basis of TRPV3 inhibition by an antagonist. Nat.Chem.Biol. (2023)

Release Date

2022-11-09

Peptides

Fusion protein of Transient receptor potential cation channel subfamily V member 3 and 3C-GFP: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

D
D

Membrane

We predict this structure to be a membrane protein.
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Fusion protein of Transient receptor potential cation channel subfamily V member 3 and 3C-GFP

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