SMTL ID : 8u4d.1

TRPV1 in nanodisc bound with PI-Br4, consensus structure

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x VPN: (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9R,10S)-9,10-dibromooctadecanoate

VPN.1: 33 residues within 4Å: Chain A: R.303, H.304, V.402, D.403, S.404, Y.405, S.406, L.409, F.410, F.416, F.437, A.440, M.441, T.444, N.445, L.447, Y.448, R.451, I.463, E.464, K.465, I.467, L.468, I.567, L.570, Q.571, I.574 Chain B: F.481, F.485, I.532, L.533, A.536, L.540 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.405, A:L.409, A:F.437, A:F.437, A:A.440, A:T.444, B:F.485 Hydrogen bonds: A:R.303, A:H.304, A:D.403, A:Y.405, A:S.406, A:S.406, A:S.406, A:E.464, A:E.464, A:K.465, A:Q.571 Salt bridges: A:R.451 VPN.3: 33 residues within 4Å: Chain B: R.303, H.304, V.402, D.403, S.404, Y.405, S.406, L.409, F.410, F.416, F.437, A.440, M.441, T.444, N.445, L.447, Y.448, R.451, I.463, E.464, K.465, I.467, L.468, I.567, L.570, Q.571, I.574 Chain D: F.481, F.485, I.532, L.533, A.536, L.540 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.405, B:L.409, B:F.437, B:F.437, B:A.440, B:T.444, D:F.485 Hydrogen bonds: B:R.303, B:H.304, B:D.403, B:Y.405, B:S.406, B:S.406, B:S.406, B:E.464, B:E.464, B:K.465, B:Q.571 Salt bridges: B:R.451 VPN.4: 33 residues within 4Å: Chain A: F.481, F.485, I.532, L.533, A.536, L.540 Chain C: R.303, H.304, V.402, D.403, S.404, Y.405, S.406, L.409, F.410, F.416, F.437, A.440, M.441, T.444, N.445, L.447, Y.448, R.451, I.463, E.464, K.465, I.467, L.468, I.567, L.570, Q.571, I.574 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.405, C:L.409, C:F.437, C:F.437, C:A.440, C:T.444, A:F.485 Hydrogen bonds: C:R.303, C:H.304, C:D.403, C:Y.405, C:S.406, C:S.406, C:S.406, C:E.464, C:E.464, C:K.465, C:Q.571 Salt bridges: C:R.451 VPN.5: 33 residues within 4Å: Chain C: F.481, F.485, I.532, L.533, A.536, L.540 Chain D: R.303, H.304, V.402, D.403, S.404, Y.405, S.406, L.409, F.410, F.416, F.437, A.440, M.441, T.444, N.445, L.447, Y.448, R.451, I.463, E.464, K.465, I.467, L.468, I.567, L.570, Q.571, I.574 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.405, D:L.409, D:F.437, D:F.437, D:A.440, D:T.444, C:F.485 Hydrogen bonds: D:R.303, D:H.304, D:D.403, D:Y.405, D:S.406, D:S.406, D:S.406, D:E.464, D:E.464, D:K.465, D:Q.571 Salt bridges: D:R.451

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

NA.2: 4 residues within 4Å: Chain A: G.514 Chain B: G.514 Chain C: G.514 Chain D: G.514 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.514

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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