SMTL ID : 8u30.1

TRPV1 in nanodisc bound with diC8-PIP2 in the closed 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: 26 residues within 4Å: Chain A: S.404, R.409, H.410, R.499, V.508, D.509, S.510, Y.511, S.512, L.515, T.550, N.551, L.553, Y.554, R.557, I.569, E.570, K.571, I.573, L.574, I.673, L.676, Q.677, I.680 Chain B: F.587, L.646 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.511, A:Y.511, A:L.515, A:L.553, A:E.570 Hydrogen bonds: A:V.508, A:S.510, A:Y.511, A:S.512, A:E.570, A:Q.677 Salt bridges: A:R.409, A:H.410, A:R.557, A:K.571 PIO.3: 23 residues within 4Å: Chain B: R.409, H.410, V.508, D.509, S.510, Y.511, S.512, L.515, T.550, N.551, L.553, Y.554, R.557, I.569, E.570, I.573, L.574, I.673, L.676, Q.677, I.680 Chain D: F.587, L.646 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.511, B:L.515, B:L.553, B:E.570, B:I.573 Hydrogen bonds: B:R.409, B:R.409, B:D.509, B:S.510, B:Y.511, B:S.512, B:I.673, B:Q.677 Salt bridges: B:H.410, B:R.557, B:R.557 PIO.4: 23 residues within 4Å: Chain A: F.587, L.646 Chain C: R.409, H.410, V.508, D.509, S.510, Y.511, S.512, L.515, T.550, N.551, L.553, Y.554, R.557, I.569, E.570, I.573, L.574, I.673, L.676, Q.677, I.680 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:Y.511, C:L.515, C:L.553, C:E.570, C:I.573 Hydrogen bonds: C:R.409, C:R.409, C:D.509, C:S.510, C:Y.511, C:S.512, C:I.673, C:Q.677 Salt bridges: C:H.410, C:R.557, C:R.557 PIO.5: 23 residues within 4Å: Chain C: F.587, L.646 Chain D: R.409, H.410, V.508, D.509, S.510, Y.511, S.512, L.515, T.550, N.551, L.553, Y.554, R.557, I.569, E.570, I.573, L.574, I.673, L.676, Q.677, I.680 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:Y.511, D:L.515, D:L.553, D:E.570, D:I.573 Hydrogen bonds: D:R.409, D:R.409, D:D.509, D:S.510, D:Y.511, D:S.512, D:I.673, D:Q.677 Salt bridges: D:H.410, D:R.557, D:R.557

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

NA.2: 8 residues within 4Å: Chain A: G.620, M.621 Chain B: G.620, M.621 Chain C: G.620, M.621 Chain D: G.620, M.621 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.620

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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