SMTL ID : 8t3m.1

TRPV1 in nanodisc bound with 3 LPA molecules

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

1 x 85R: [(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{S},3~{S},5~{R},6~{S})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate(Non-covalent)

85R.1: 29 residues within 4Å: Chain A: S.300, R.305, H.306, V.404, D.405, S.406, Y.407, S.408, L.411, F.439, A.442, M.443, T.446, N.447, L.449, Y.450, R.453, E.466, I.469, L.470, I.569, L.572, Q.573, I.576 Chain B: F.483, F.487, L.535, A.538, L.542 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.407, A:L.411, A:A.442, A:M.443, A:E.466, A:I.469, B:F.487, B:L.535 Hydrogen bonds: A:R.305, A:S.406, A:Y.407, A:S.408, A:Q.573 Salt bridges: A:R.453

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

NA.2: 7 residues within 4Å: Chain A: G.516, M.517 Chain B: G.516, M.517 Chain C: G.516 Chain D: G.516, M.517 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.516 NA.3: 4 residues within 4Å: Chain A: G.516 Chain B: G.516 Chain C: G.516 Chain D: G.516 No protein-ligand interaction detected (PLIP)

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

NKN.4: 18 residues within 4Å: Chain B: Y.407, S.408, L.411, F.412, F.439, A.442, M.443, T.446, N.447, L.449, Y.450, E.466 Chain D: F.483, F.487, I.534, L.535, A.538, L.542 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:F.487, D:L.542, B:F.439, B:A.442, B:T.446 Hydrogen bonds: B:T.446 NKN.5: 21 residues within 4Å: Chain A: F.483, F.487, I.534, L.535, A.538, L.542 Chain C: Y.407, S.408, L.411, F.418, F.439, A.442, M.443, T.446, N.447, L.449, Y.450, R.453, I.465, E.466, I.469 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.411, C:F.418, C:F.439, C:F.439, C:T.446, A:F.487, A:A.538 Hydrogen bonds: C:Y.407, C:S.408, C:S.408, C:R.453 NKN.6: 20 residues within 4Å: Chain C: F.483, F.487, I.534, L.535, A.538, L.542 Chain D: Y.407, S.408, L.411, F.439, A.442, M.443, T.446, N.447, L.449, Y.450, R.453, I.465, E.466, I.469 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.439, D:F.439, D:T.446, C:F.487, C:I.534, C:L.542 Hydrogen bonds: D:T.446, D:N.447

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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