SMTL ID : 8sly.1

Rat TRPV2 bound with 2 CBD ligands in nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x P0T: cannabidiol(Non-covalent)

P0T.1: 11 residues within 4Å: Chain A: L.534, L.537, L.538, F.540, L.541, Y.544, L.637, M.640 Chain D: L.631, Y.634, V.635 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain A Hydrophobic interactions: D:L.631, D:Y.634, D:V.635, A:L.534, A:L.537, A:L.537, A:L.537, A:L.538, A:L.541, A:L.541, A:Y.544, A:L.637 P0T.2: 9 residues within 4Å: Chain A: M.468, Y.471, I.524, Q.530, I.533, L.534 Chain D: V.635, N.639 Ligands: POV.4 9 PLIP interactions: 1 interactions with chain D, 8 interactions with chain A Hydrophobic interactions: D:V.635, A:Y.471, A:I.524, A:I.524, A:Q.530, A:I.533, A:I.533, A:L.534 Hydrogen bonds: A:L.534 P0T.5: 11 residues within 4Å: Chain A: L.631, Y.634, V.635 Chain B: L.534, L.537, L.538, F.540, L.541, Y.544, L.637, M.640 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.534, B:L.537, B:L.537, B:L.537, B:L.538, B:L.541, B:L.541, B:Y.544, B:L.637, A:L.631, A:Y.634, A:V.635 P0T.6: 9 residues within 4Å: Chain A: V.635, N.639 Chain B: M.468, Y.471, I.524, Q.530, I.533, L.534 Ligands: POV.7 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.471, B:I.524, B:I.524, B:Q.530, B:I.533, B:I.533, B:L.534, A:V.635 Hydrogen bonds: B:L.534 P0T.8: 11 residues within 4Å: Chain B: L.631, Y.634, V.635 Chain C: L.534, L.537, L.538, F.540, L.541, Y.544, L.637, M.640 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:L.631, B:Y.634, B:V.635, C:L.534, C:L.537, C:L.537, C:L.537, C:L.538, C:L.541, C:L.541, C:Y.544, C:L.637 P0T.9: 11 residues within 4Å: Chain B: V.635, L.638, N.639, I.642 Chain C: M.468, Y.471, I.524, Q.530, I.533, L.534 Ligands: POV.10 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:V.635, B:L.638, B:I.642, C:Y.471, C:I.524, C:I.524, C:Q.530, C:I.533, C:I.533, C:L.534 Hydrogen bonds: C:L.534 P0T.11: 11 residues within 4Å: Chain C: L.631, Y.634, V.635 Chain D: L.534, L.537, L.538, F.540, L.541, Y.544, L.637, M.640 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.534, D:L.537, D:L.537, D:L.537, D:L.538, D:L.541, D:L.541, D:Y.544, D:L.637, C:L.631, C:Y.634, C:V.635 P0T.12: 9 residues within 4Å: Chain C: V.635, N.639 Chain D: M.468, Y.471, I.524, Q.530, I.533, L.534 Ligands: POV.13 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.471, D:I.524, D:I.524, D:Q.530, D:I.533, D:I.533, D:L.534, C:V.635, C:N.639 Hydrogen bonds: D:L.534

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

NA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

POV.4: 16 residues within 4Å: Chain A: Y.471, F.472, L.475, L.510, L.513, H.521, T.522, G.523, I.524, Y.525, Q.530, Q.663 Chain D: V.635, L.636, N.639 Ligands: P0T.2 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:Y.471, A:F.472, A:L.510, D:V.635, D:L.636 Hydrogen bonds: A:Y.471, A:Q.530, A:Q.530, A:Q.663, D:N.639 pi-Cation interactions: A:Y.525 POV.7: 16 residues within 4Å: Chain A: V.635, L.636, N.639 Chain B: Y.471, F.472, L.475, L.510, L.513, H.521, T.522, G.523, I.524, Y.525, Q.530, Q.663 Ligands: P0T.6 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:V.635, A:L.636, B:Y.471, B:F.472, B:L.510 Hydrogen bonds: A:N.639, B:Y.471, B:Q.530, B:Q.530, B:Q.663 pi-Cation interactions: B:Y.525 POV.10: 16 residues within 4Å: Chain B: V.635, L.636, N.639 Chain C: Y.471, F.472, L.475, L.510, L.513, H.521, T.522, G.523, I.524, Y.525, Q.530, Q.663 Ligands: P0T.9 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Y.471, C:F.472, C:L.510, B:V.635, B:L.636 Hydrogen bonds: C:Y.471, C:Q.530, C:Q.530, C:Q.663, B:N.639 pi-Cation interactions: C:Y.525 POV.13: 16 residues within 4Å: Chain C: V.635, L.636, N.639 Chain D: Y.471, F.472, L.475, L.510, L.513, H.521, T.522, G.523, I.524, Y.525, Q.530, Q.663 Ligands: P0T.12 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.471, D:F.472, D:L.510, C:V.635, C:L.636 Hydrogen bonds: D:Y.471, D:Q.530, D:Q.530, D:Q.663, C:N.639 pi-Cation interactions: D:Y.525

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gochman, A. et al., Cannabidiol sensitizes TRPV2 channels to activation by 2-APB. Elife (2023)

Release Date

2023-05-31

Peptides

Transient receptor potential cation channel subfamily V member 2: 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 2

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