SMTL ID : 8t0e.1

TRPV1 in Nanodisc not bound with lysophosphatidic acid (apo)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 8IJ: (2R)-3-{[(R)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate(Non-covalent)

8IJ.1: 29 residues within 4Å: Chain A: R.409, H.410, D.509, S.510, Y.511, S.512, I.514, L.515, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, E.570, K.571, I.573, L.574, I.673, L.676, Q.677, I.680 Chain B: F.587, F.591, L.639, A.642, L.646 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.511, A:Y.511, A:L.515, A:F.543, A:L.553, A:I.573, B:F.591 Hydrogen bonds: A:D.509, A:Y.511, A:S.512, A:E.570, A:E.570, A:Q.677 Salt bridges: A:R.557 8IJ.3: 29 residues within 4Å: Chain B: R.409, H.410, D.509, S.510, Y.511, S.512, I.514, L.515, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, E.570, K.571, I.573, L.574, I.673, L.676, Q.677, I.680 Chain D: F.587, F.591, L.639, A.642, L.646 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.511, B:Y.511, B:L.515, B:F.543, B:L.553, B:I.573, D:F.591 Hydrogen bonds: B:D.509, B:Y.511, B:S.512, B:E.570, B:E.570, B:Q.677 Salt bridges: B:R.557 8IJ.4: 29 residues within 4Å: Chain A: F.587, F.591, L.639, A.642, L.646 Chain C: R.409, H.410, D.509, S.510, Y.511, S.512, I.514, L.515, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, E.570, K.571, I.573, L.574, I.673, L.676, Q.677, I.680 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.511, C:Y.511, C:L.515, C:F.543, C:L.553, C:I.573, A:F.591 Hydrogen bonds: C:D.509, C:Y.511, C:S.512, C:E.570, C:E.570, C:Q.677 Salt bridges: C:R.557 8IJ.5: 29 residues within 4Å: Chain C: F.587, F.591, L.639, A.642, L.646 Chain D: R.409, H.410, D.509, S.510, Y.511, S.512, I.514, L.515, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, E.570, K.571, I.573, L.574, I.673, L.676, Q.677, I.680 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.511, D:Y.511, D:L.515, D:F.543, D:L.553, D:I.573, C:F.591 Hydrogen bonds: D:D.509, D:Y.511, D:S.512, D:E.570, D:E.570, D:Q.677 Salt bridges: D:R.557

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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