SMTL ID : 8u2z.1

TRPV1 in nanodisc bound with diC8-PIP2 in the dilated state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.1: 23 residues within 4Å: Chain A: Y.405, S.406, L.409, F.416, F.437, A.440, M.441, T.444, N.445, L.447, Y.448, R.451, I.463, I.467, L.471 Chain B: F.485, I.532, L.533, L.535, A.536, I.539, L.540 Ligands: PCW.2 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.416, A:F.437, A:F.437, A:A.440, B:F.485, B:I.532, B:L.533 Hydrogen bonds: A:Y.405, A:Y.405, A:N.445, A:N.445, A:R.451 PIO.6: 23 residues within 4Å: Chain B: Y.405, S.406, L.409, F.416, F.437, A.440, M.441, T.444, N.445, L.447, Y.448, R.451, I.463, I.467, L.471 Chain D: F.485, I.532, L.533, L.535, A.536, I.539, L.540 Ligands: PCW.11 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:F.416, B:F.437, B:F.437, B:A.440, D:F.485, D:I.532, D:L.533, D:I.539 Hydrogen bonds: B:Y.405, B:Y.405, B:N.445, B:N.445, B:R.451 PIO.7: 23 residues within 4Å: Chain A: F.485, I.532, L.533, L.535, A.536, I.539, L.540 Chain C: Y.405, S.406, L.409, F.416, F.437, A.440, M.441, T.444, N.445, L.447, Y.448, R.451, I.463, I.467, L.471 Ligands: PCW.8 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:F.416, C:F.437, C:F.437, C:A.440, A:F.485, A:I.532, A:A.536, A:I.539, A:I.539 Hydrogen bonds: C:Y.405, C:Y.405, C:N.445, C:N.445, C:R.451 PIO.13: 23 residues within 4Å: Chain C: F.485, I.532, L.533, L.535, A.536, I.539, L.540 Chain D: Y.405, S.406, L.409, F.416, F.437, A.440, M.441, T.444, N.445, L.447, Y.448, R.451, I.463, I.467, L.471 Ligands: PCW.9 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:F.485, C:I.532, C:L.533, C:I.539, D:F.416, D:F.437, D:F.437, D:A.440 Hydrogen bonds: D:Y.405, D:Y.405, D:N.445, D:N.445, D:R.451

4 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.2: 26 residues within 4Å: Chain A: F.474, M.475, Y.478, L.479, L.482, Y.502, C.505, L.506, F.509, K.510, T.512, I.513, M.515, T.541, Y.542, L.545 Chain B: F.511, T.521, K.527, I.531, L.534, L.535, V.538, I.539 Ligands: PIO.1, CLR.5 18 PLIP interactions: 7 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:L.534, B:L.534, B:L.535, B:V.538, B:I.539, A:F.474, A:Y.478, A:L.482, A:Y.502, A:L.506, A:F.509, A:F.509, A:F.509, A:F.509, A:I.513, A:L.545 Hydrogen bonds: B:T.521 Salt bridges: B:K.527 PCW.8: 26 residues within 4Å: Chain A: F.511, T.521, K.527, I.531, L.534, L.535, V.538, I.539 Chain C: F.474, M.475, Y.478, L.479, L.482, Y.502, C.505, L.506, F.509, K.510, T.512, I.513, M.515, T.541, Y.542, L.545 Ligands: CLR.3, PIO.7 17 PLIP interactions: 6 interactions with chain A, 11 interactions with chain C Hydrophobic interactions: A:L.534, A:L.535, A:V.538, A:I.539, C:F.474, C:Y.478, C:L.482, C:Y.502, C:L.506, C:F.509, C:F.509, C:F.509, C:F.509, C:I.513, C:L.545 Hydrogen bonds: A:T.521 Salt bridges: A:K.527 PCW.9: 26 residues within 4Å: Chain C: F.511, T.521, K.527, I.531, L.534, L.535, V.538, I.539 Chain D: F.474, M.475, Y.478, L.479, L.482, Y.502, C.505, L.506, F.509, K.510, T.512, I.513, M.515, T.541, Y.542, L.545 Ligands: CLR.10, PIO.13 20 PLIP interactions: 11 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:F.474, D:Y.478, D:L.482, D:Y.502, D:L.506, D:F.509, D:F.509, D:F.509, D:F.509, D:I.513, D:L.545, C:I.531, C:L.534, C:L.534, C:L.535, C:L.535, C:V.538, C:I.539 Hydrogen bonds: C:T.521 Salt bridges: C:K.527 PCW.11: 26 residues within 4Å: Chain B: F.474, M.475, Y.478, L.479, L.482, Y.502, C.505, L.506, F.509, K.510, T.512, I.513, M.515, T.541, Y.542, L.545 Chain D: F.511, T.521, K.527, I.531, L.534, L.535, V.538, I.539 Ligands: PIO.6, CLR.12 19 PLIP interactions: 11 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: B:F.474, B:Y.478, B:L.482, B:Y.502, B:L.506, B:F.509, B:F.509, B:F.509, B:F.509, B:I.513, B:L.545, D:L.534, D:L.534, D:L.535, D:L.535, D:V.538, D:I.539 Hydrogen bonds: D:T.521 Salt bridges: D:K.527

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 20 residues within 4Å: Chain A: F.511, T.512, I.513, G.514, V.538, I.539, Y.542, I.543, L.546 Chain C: M.466, D.470, L.471, F.474, M.475, I.513, L.545, M.548, L.549, L.552 Ligands: PCW.8 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:V.538, A:I.539, A:Y.542, A:Y.542, A:Y.542, A:I.543, A:L.546, C:F.474, C:F.474, C:I.513, C:L.545, C:M.548 Hydrogen bonds: A:T.512 CLR.5: 20 residues within 4Å: Chain A: M.466, D.470, L.471, F.474, M.475, I.513, L.545, M.548, L.549, L.552 Chain B: F.511, T.512, I.513, G.514, V.538, I.539, Y.542, I.543, L.546 Ligands: PCW.2 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.539, B:Y.542, B:Y.542, B:I.543, A:F.474, A:F.474, A:I.513, A:L.545, A:M.548 Hydrogen bonds: B:T.512 CLR.10: 20 residues within 4Å: Chain C: F.511, T.512, I.513, G.514, V.538, I.539, Y.542, I.543, L.546 Chain D: M.466, D.470, L.471, F.474, M.475, I.513, L.545, M.548, L.549, L.552 Ligands: PCW.9 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:F.474, D:F.474, D:I.513, D:L.545, D:M.548, C:I.539, C:Y.542, C:Y.542, C:Y.542, C:I.543, C:L.546 Hydrogen bonds: C:T.512 CLR.12: 20 residues within 4Å: Chain B: M.466, D.470, L.471, F.474, M.475, I.513, L.545, M.548, L.549, L.552 Chain D: F.511, T.512, I.513, G.514, V.538, I.539, Y.542, I.543, L.546 Ligands: PCW.11 12 PLIP interactions: 7 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:I.539, D:Y.542, D:Y.542, D:Y.542, D:I.543, D:L.546, B:F.474, B:F.474, B:I.513, B:L.545, B:M.548 Hydrogen bonds: D:T.512

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

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arnold, W.R. et al., Structural basis of TRPV1 modulation by endogenous bioactive lipids. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-05-08

Peptides

Transient receptor potential cation channel subfamily V member 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily V member 1

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