SMTL ID : 8u3l.1

TRPV1 in nanodisc bound with empty vanilloid binding pocket at 25C

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.1: 19 residues within 4Å: Chain A: Y.511, L.515, F.522, V.525, E.536, A.539, S.540, F.543, A.546, M.547, T.550 Chain B: F.591, F.632, A.634, V.635, I.638, L.639, A.642, L.646 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.522, A:F.543, A:F.543, A:F.543, B:I.638 3PH.3: 19 residues within 4Å: Chain B: Y.511, L.515, F.522, V.525, E.536, A.539, S.540, F.543, A.546, M.547, T.550 Chain D: F.591, F.632, A.634, V.635, I.638, L.639, A.642, L.646 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:F.522, B:F.543, B:F.543, B:F.543, D:I.638 3PH.4: 19 residues within 4Å: Chain A: F.591, F.632, A.634, V.635, I.638, L.639, A.642, L.646 Chain C: Y.511, L.515, F.522, V.525, E.536, A.539, S.540, F.543, A.546, M.547, T.550 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:I.638, C:F.522, C:F.543, C:F.543, C:F.543 3PH.5: 19 residues within 4Å: Chain C: F.591, F.632, A.634, V.635, I.638, L.639, A.642, L.646 Chain D: Y.511, L.515, F.522, V.525, E.536, A.539, S.540, F.543, A.546, M.547, T.550 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.522, D:F.543, D:F.543, D:F.543, C:I.638

1 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

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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