SMTL ID : 8t10.1

TRPV1 in nanodisc bound with two LPA molecules in opposite monomers

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

2 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: 32 residues within 4Å: Chain A: R.409, H.410, F.507, V.508, D.509, S.510, Y.511, S.512, I.514, L.515, V.518, 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 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.514, A:L.515, A:L.515, A:L.515, A:A.546, A:T.550, B:F.591 Hydrogen bonds: A:S.510, A:S.510, A:Y.511, A:S.512, A:E.570, A:Q.677 Salt bridges: A:R.557, A:R.557 8IJ.5: 31 residues within 4Å: Chain C: S.404, R.409, H.410, F.507, D.509, S.510, Y.511, S.512, E.513, I.514, L.515, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, E.570, I.573, L.574, I.673, L.676, Q.677, I.680 Chain D: F.587, F.591, L.639, A.642, L.646 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.507, C:Y.511, C:I.514, C:L.515, C:F.543, C:A.546, C:L.553, D:L.639 Hydrogen bonds: C:R.409, C:S.510, C:Y.511, C:S.512, C:S.512, C:R.557, C:E.570, C:Q.677 Salt bridges: C:R.557

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

NA.2: 7 residues within 4Å: Chain A: G.620, Y.648 Chain B: G.620 Chain C: G.620, Y.648 Chain D: G.620 Ligands: NA.4 No protein-ligand interaction detected (PLIP) NA.4: 5 residues within 4Å: Chain A: G.620 Chain B: G.620 Chain C: G.620 Chain D: G.620 Ligands: NA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.620

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

NKN.3: 20 residues within 4Å: Chain B: Y.511, S.512, L.515, V.518, F.522, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, Q.677 Chain C: F.587, F.591, I.638, L.639, A.642, L.646 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.522, B:F.543, B:A.546, B:T.550, C:F.591, C:F.591, C:L.639 Hydrogen bonds: B:Y.511, B:S.512, B:S.512, B:S.512, B:Q.677 Salt bridges: B:R.557 NKN.6: 19 residues within 4Å: Chain A: F.591, I.638, L.639, A.642, L.646 Chain D: Y.511, S.512, L.515, F.516, F.522, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, I.573 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.543, D:F.543, D:F.543, D:A.546, A:F.591, A:I.638, A:A.642 Hydrogen bonds: D:Y.511, D:Y.511, D:T.550 Salt bridges: D:R.557

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
B

B
A

C
D

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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