SMTL ID : 8sp8.1

Human TRP channel TRPV6 in cNW30 nanodiscs inhibited by tetrahydrocannabivarin (THCV)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 21 residues within 4Å: Chain A: F.329, L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, F.425, H.426, I.429, Y.467, F.468, T.600, M.603, L.604, K.607 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.332, A:I.335, A:Y.339, A:I.394, A:I.399, A:V.402, A:F.425, A:I.429, A:Y.467, A:F.468, A:L.604 Hydrogen bonds: A:Y.467, A:Y.467 Salt bridges: A:H.426, A:H.426, A:K.607, A:K.607 Y01.2: 25 residues within 4Å: Chain A: G.422, P.424, F.425, L.428, S.455, F.456, V.459, L.460, C.463, N.464, M.466, Y.467, T.479, I.482, Q.483 Chain B: L.496, F.504, M.554, I.557, T.558, A.561, I.565 Ligands: POV.4, POV.15, I8E.16 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:I.557, B:T.558, B:A.561, B:I.565, A:F.456, A:F.456, A:V.459, A:L.460, A:M.466, A:Y.467 Hydrogen bonds: A:F.425, A:T.479, A:Q.483 Y01.3: 22 residues within 4Å: Chain A: F.493, C.494, M.497, A.498, I.501, Y.524, D.525, P.527, M.528, L.530, F.531, F.534 Chain B: F.553, S.556, I.557, A.560, I.564 Ligands: POV.5, POV.6, I8E.8, POV.15, I8E.16 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.531, A:F.534, A:F.534, B:I.557, B:A.560 Hydrogen bonds: A:Y.524, A:D.525 Y01.17: 21 residues within 4Å: Chain B: F.329, L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, F.425, H.426, I.429, Y.467, F.468, T.600, M.603, L.604, K.607 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.332, B:I.335, B:Y.339, B:I.394, B:I.399, B:V.402, B:F.425, B:I.429, B:Y.467, B:F.468, B:L.604 Hydrogen bonds: B:Y.467, B:Y.467 Salt bridges: B:H.426, B:H.426, B:K.607, B:K.607 Y01.18: 25 residues within 4Å: Chain B: G.422, P.424, F.425, L.428, S.455, F.456, V.459, L.460, C.463, N.464, M.466, Y.467, T.479, I.482, Q.483 Chain C: L.496, F.504, M.554, I.557, T.558, A.561, I.565 Ligands: POV.20, POV.27, I8E.28 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.456, B:F.456, B:V.459, B:L.460, B:M.466, B:Y.467, C:I.557, C:T.558, C:A.561, C:I.565 Hydrogen bonds: B:F.425, B:T.479, B:Q.483 Y01.19: 22 residues within 4Å: Chain B: F.493, C.494, M.497, A.498, I.501, Y.524, D.525, P.527, M.528, L.530, F.531, F.534 Chain C: F.553, S.556, I.557, A.560, I.564 Ligands: POV.21, POV.22, I8E.24, POV.27, I8E.28 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.531, B:F.534, B:F.534, C:I.557, C:A.560 Hydrogen bonds: B:Y.524, B:D.525 Y01.29: 21 residues within 4Å: Chain C: F.329, L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, F.425, H.426, I.429, Y.467, F.468, T.600, M.603, L.604, K.607 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.332, C:I.335, C:Y.339, C:I.394, C:I.399, C:V.402, C:F.425, C:I.429, C:Y.467, C:F.468, C:L.604 Hydrogen bonds: C:Y.467, C:Y.467 Salt bridges: C:H.426, C:H.426, C:K.607, C:K.607 Y01.30: 25 residues within 4Å: Chain C: G.422, P.424, F.425, L.428, S.455, F.456, V.459, L.460, C.463, N.464, M.466, Y.467, T.479, I.482, Q.483 Chain D: L.496, F.504, M.554, I.557, T.558, A.561, I.565 Ligands: POV.32, POV.41, I8E.42 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:I.557, D:A.561, D:I.565, C:F.456, C:F.456, C:V.459, C:L.460, C:M.466, C:Y.467 Hydrogen bonds: C:F.425, C:T.479, C:Q.483 Y01.31: 22 residues within 4Å: Chain C: F.493, C.494, M.497, A.498, I.501, Y.524, D.525, P.527, M.528, L.530, F.531, F.534 Chain D: F.553, S.556, I.557, A.560, I.564 Ligands: POV.33, POV.34, I8E.36, POV.41, I8E.42 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.531, C:F.534, C:F.534, D:I.557, D:A.560 Hydrogen bonds: C:Y.524, C:D.525 Y01.43: 21 residues within 4Å: Chain D: F.329, L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, F.425, H.426, I.429, Y.467, F.468, T.600, M.603, L.604, K.607 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.332, D:I.335, D:Y.339, D:I.394, D:I.399, D:V.402, D:F.425, D:I.429, D:Y.467, D:F.468, D:L.604 Hydrogen bonds: D:Y.467, D:Y.467 Salt bridges: D:H.426, D:H.426, D:K.607, D:K.607 Y01.44: 25 residues within 4Å: Chain A: L.496, F.504, M.554, I.557, T.558, A.561, I.565 Chain D: G.422, P.424, F.425, L.428, S.455, F.456, V.459, L.460, C.463, N.464, M.466, Y.467, T.479, I.482, Q.483 Ligands: POV.11, I8E.12, POV.46 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.456, D:F.456, D:V.459, D:L.460, D:M.466, D:Y.467, A:I.557, A:A.561, A:I.565 Hydrogen bonds: D:F.425, D:T.479, D:Q.483 Y01.45: 22 residues within 4Å: Chain A: F.553, S.556, I.557, A.560, I.564 Chain D: F.493, C.494, M.497, A.498, I.501, Y.524, D.525, P.527, M.528, L.530, F.531, F.534 Ligands: POV.11, I8E.12, POV.47, POV.48, I8E.50 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:F.531, D:F.534, D:F.534, A:I.557, A:A.560 Hydrogen bonds: D:Y.524, D:D.525

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

POV.4: 26 residues within 4Å: Chain A: R.350, L.352, Q.369, Q.370, T.431, F.434, M.435, L.437, V.438, V.441, M.442, I.445, A.447, S.448, G.449, E.450, V.451, V.452, P.453, F.456, L.460 Chain B: T.514, F.553 Ligands: Y01.2, POV.15, I8E.16 Ligand excluded by PLIP POV.5: 5 residues within 4Å: Chain A: P.527, L.530 Ligands: Y01.3, POV.6, POV.15 Ligand excluded by PLIP POV.6: 24 residues within 4Å: Chain A: M.491, C.494, W.495, A.498, V.499, L.502, Y.509, Q.513, D.525, Y.526, P.527, L.530 Chain D: L.337, I.341, T.344, M.345, I.348, Y.349, W.462, V.465 Ligands: Y01.3, POV.5, POV.15, POV.39 Ligand excluded by PLIP POV.7: 17 residues within 4Å: Chain A: F.343, C.346, C.347, L.373, Q.374, Y.377, L.386, E.389, L.390, T.392, V.393, V.436, T.439, M.440, R.443, L.444, M.454 Ligand excluded by PLIP POV.9: 6 residues within 4Å: Chain A: L.338, I.341, M.345, Y.349 Ligands: POV.10, POV.22 Ligand excluded by PLIP POV.10: 10 residues within 4Å: Chain A: C.342, M.345, C.346, Y.349, K.381, I.384, R.385, V.387, G.388 Ligands: POV.9 Ligand excluded by PLIP POV.11: 16 residues within 4Å: Chain A: E.515, D.550, L.551, P.552, F.553, I.557 Chain D: D.364, T.366, V.452, F.456 Ligands: I8E.12, Y01.44, Y01.45, POV.46, POV.47, POV.48 Ligand excluded by PLIP POV.15: 17 residues within 4Å: Chain A: D.364, T.366, V.452, F.456 Chain B: E.515, D.550, L.551, P.552, F.553, M.554, I.557 Ligands: Y01.2, Y01.3, POV.4, POV.5, POV.6, I8E.16 Ligand excluded by PLIP POV.20: 26 residues within 4Å: Chain B: R.350, L.352, Q.369, Q.370, T.431, F.434, M.435, L.437, V.438, V.441, M.442, I.445, A.447, S.448, G.449, E.450, V.451, V.452, P.453, F.456, L.460 Chain C: T.514, F.553 Ligands: Y01.18, POV.27, I8E.28 Ligand excluded by PLIP POV.21: 5 residues within 4Å: Chain B: P.527, L.530 Ligands: Y01.19, POV.22, POV.27 Ligand excluded by PLIP POV.22: 24 residues within 4Å: Chain A: L.337, I.341, T.344, M.345, I.348, Y.349, W.462, V.465 Chain B: M.491, C.494, W.495, A.498, V.499, L.502, Y.509, Q.513, D.525, Y.526, P.527, L.530 Ligands: POV.9, Y01.19, POV.21, POV.27 Ligand excluded by PLIP POV.23: 17 residues within 4Å: Chain B: F.343, C.346, C.347, L.373, Q.374, Y.377, L.386, E.389, L.390, T.392, V.393, V.436, T.439, M.440, R.443, L.444, M.454 Ligand excluded by PLIP POV.25: 6 residues within 4Å: Chain B: L.338, I.341, M.345, Y.349 Ligands: POV.26, POV.34 Ligand excluded by PLIP POV.26: 10 residues within 4Å: Chain B: C.342, M.345, C.346, Y.349, K.381, I.384, R.385, V.387, G.388 Ligands: POV.25 Ligand excluded by PLIP POV.27: 17 residues within 4Å: Chain B: D.364, T.366, V.452, F.456 Chain C: E.515, D.550, L.551, P.552, F.553, M.554, I.557 Ligands: Y01.18, Y01.19, POV.20, POV.21, POV.22, I8E.28 Ligand excluded by PLIP POV.32: 26 residues within 4Å: Chain C: R.350, L.352, Q.369, Q.370, T.431, F.434, M.435, L.437, V.438, V.441, M.442, I.445, A.447, S.448, G.449, E.450, V.451, V.452, P.453, F.456, L.460 Chain D: T.514, F.553 Ligands: Y01.30, POV.41, I8E.42 Ligand excluded by PLIP POV.33: 5 residues within 4Å: Chain C: P.527, L.530 Ligands: Y01.31, POV.34, POV.41 Ligand excluded by PLIP POV.34: 24 residues within 4Å: Chain B: L.337, I.341, T.344, M.345, I.348, Y.349, W.462, V.465 Chain C: M.491, C.494, W.495, A.498, V.499, L.502, Y.509, Q.513, D.525, Y.526, P.527, L.530 Ligands: POV.25, Y01.31, POV.33, POV.41 Ligand excluded by PLIP POV.35: 17 residues within 4Å: Chain C: F.343, C.346, C.347, L.373, Q.374, Y.377, L.386, E.389, L.390, T.392, V.393, V.436, T.439, M.440, R.443, L.444, M.454 Ligand excluded by PLIP POV.37: 6 residues within 4Å: Chain C: L.338, I.341, M.345, Y.349 Ligands: POV.38, POV.48 Ligand excluded by PLIP POV.38: 10 residues within 4Å: Chain C: C.342, M.345, C.346, Y.349, K.381, I.384, R.385, V.387, G.388 Ligands: POV.37 Ligand excluded by PLIP POV.39: 6 residues within 4Å: Chain D: L.338, I.341, M.345, Y.349 Ligands: POV.6, POV.40 Ligand excluded by PLIP POV.40: 10 residues within 4Å: Chain D: C.342, M.345, C.346, Y.349, K.381, I.384, R.385, V.387, G.388 Ligands: POV.39 Ligand excluded by PLIP POV.41: 17 residues within 4Å: Chain C: D.364, T.366, V.452, F.456 Chain D: E.515, D.550, L.551, P.552, F.553, M.554, I.557 Ligands: Y01.30, Y01.31, POV.32, POV.33, POV.34, I8E.42 Ligand excluded by PLIP POV.46: 26 residues within 4Å: Chain A: T.514, F.553 Chain D: R.350, L.352, Q.369, Q.370, T.431, F.434, M.435, L.437, V.438, V.441, M.442, I.445, A.447, S.448, G.449, E.450, V.451, V.452, P.453, F.456, L.460 Ligands: POV.11, I8E.12, Y01.44 Ligand excluded by PLIP POV.47: 5 residues within 4Å: Chain D: P.527, L.530 Ligands: POV.11, Y01.45, POV.48 Ligand excluded by PLIP POV.48: 24 residues within 4Å: Chain C: L.337, I.341, T.344, M.345, I.348, Y.349, W.462, V.465 Chain D: M.491, C.494, W.495, A.498, V.499, L.502, Y.509, Q.513, D.525, Y.526, P.527, L.530 Ligands: POV.11, POV.37, Y01.45, POV.47 Ligand excluded by PLIP POV.49: 17 residues within 4Å: Chain D: F.343, C.346, C.347, L.373, Q.374, Y.377, L.386, E.389, L.390, T.392, V.393, V.436, T.439, M.440, R.443, L.444, M.454 Ligand excluded by PLIP

8 x I8E: Tetrahydrocannabivarin(Non-covalent)

I8E.8: 19 residues within 4Å: Chain A: I.486, L.490, M.491, F.493, C.494, M.497, F.534, F.537, L.538, M.570, L.573, M.577 Chain B: A.563, I.564, T.567, L.568, L.571 Ligands: Y01.3, I8E.16 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.564, B:T.567, B:L.568, B:L.571, A:L.490, A:L.490, A:F.493, A:F.534, A:L.573 I8E.12: 16 residues within 4Å: Chain A: I.557, A.560, A.561, I.564, I.565, L.568 Chain D: F.456, I.482, I.486, L.490, F.534 Ligands: POV.11, Y01.44, Y01.45, POV.46, I8E.50 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.560, A:I.564, A:I.564 I8E.16: 16 residues within 4Å: Chain A: F.456, I.482, I.486, L.490, F.534 Chain B: I.557, A.560, A.561, I.564, I.565, L.568 Ligands: Y01.2, Y01.3, POV.4, I8E.8, POV.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.560, B:I.564, B:I.564, B:I.565 I8E.24: 19 residues within 4Å: Chain B: I.486, L.490, M.491, F.493, C.494, M.497, F.534, F.537, L.538, M.570, L.573, M.577 Chain C: A.563, I.564, T.567, L.568, L.571 Ligands: Y01.19, I8E.28 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:I.564, C:T.567, C:L.568, C:L.571, B:L.490, B:L.490, B:F.493, B:F.534, B:L.573 I8E.28: 16 residues within 4Å: Chain B: F.456, I.482, I.486, L.490, F.534 Chain C: I.557, A.560, A.561, I.564, I.565, L.568 Ligands: Y01.18, Y01.19, POV.20, I8E.24, POV.27 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.560, C:I.564, C:I.564 I8E.36: 19 residues within 4Å: Chain C: I.486, L.490, M.491, F.493, C.494, M.497, F.534, F.537, L.538, M.570, L.573, M.577 Chain D: A.563, I.564, T.567, L.568, L.571 Ligands: Y01.31, I8E.42 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:I.564, D:T.567, D:L.568, D:L.571, C:L.490, C:L.490, C:F.493, C:F.534, C:L.573 I8E.42: 16 residues within 4Å: Chain C: F.456, I.482, I.486, L.490, F.534 Chain D: I.557, A.560, A.561, I.564, I.565, L.568 Ligands: Y01.30, Y01.31, POV.32, I8E.36, POV.41 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:A.560, D:I.564, D:I.564, D:I.565 I8E.50: 19 residues within 4Å: Chain A: A.563, I.564, T.567, L.568, L.571 Chain D: I.486, L.490, M.491, F.493, C.494, M.497, F.534, F.537, L.538, M.570, L.573, M.577 Ligands: I8E.12, Y01.45 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:I.564, A:T.567, A:L.568, A:L.571, D:L.490, D:L.490, D:F.493, D:F.534, D:L.573

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 4 residues within 4Å: Chain A: D.542 Chain B: D.542 Chain C: D.542 Chain D: D.542 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:D.542, C:D.542, D:D.542, A:D.542, B:D.542

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

CL.14: 8 residues within 4Å: Chain A: L.574, M.578 Chain B: L.574, M.578 Chain C: L.574, M.578 Chain D: L.574, M.578 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neuberger, A. et al., Molecular pathway and structural mechanism of human oncochannel TRPV6 inhibition by the phytocannabinoid tetrahydrocannabivarin. Nat Commun (2023)

Release Date

2023-08-23

Peptides

Transient receptor potential cation channel subfamily V member 6: 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 6