SMTL ID : 8t0c.1

TRPV1 in Nanodisc bound with lysophosphatidic acid in all four monomers

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x NKN: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate(Non-covalent)

NKN.1: 19 residues within 4Å: Chain A: Y.511, S.512, L.515, F.522, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, I.569, I.573 Chain B: F.587, F.591, I.638, L.639, A.642, L.646 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.543 Hydrogen bonds: A:Y.511, A:T.550, A:N.551, A:N.551 NKN.4: 19 residues within 4Å: Chain B: Y.511, S.512, L.515, F.522, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, I.569, I.573 Chain D: F.587, F.591, I.638, L.639, A.642, L.646 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.543 Hydrogen bonds: B:Y.511, B:T.550, B:N.551, B:N.551 NKN.5: 19 residues within 4Å: Chain A: F.587, F.591, I.638, L.639, A.642, L.646 Chain C: Y.511, S.512, L.515, F.522, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, I.569, I.573 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.543 Hydrogen bonds: C:Y.511, C:T.550, C:N.551, C:N.551 NKN.6: 19 residues within 4Å: Chain C: F.587, F.591, I.638, L.639, A.642, L.646 Chain D: Y.511, S.512, L.515, F.522, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, I.569, I.573 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.543 Hydrogen bonds: D:Y.511, D:T.550, D:N.551, D:N.551

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

NA.2: 4 residues within 4Å: Chain A: G.620 Chain B: G.620 Chain C: G.620 Chain D: G.620 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.620 NA.3: 4 residues within 4Å: Chain A: G.620 Chain B: G.620 Chain C: G.620 Chain D: G.620 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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