SMTL ID : 8t3l.1

TRPV1 in nanodisc bound with 2 LPA molecules in neighboring 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: 23 residues within 4Å: Chain A: R.305, H.306, D.405, S.406, Y.407, S.408, L.411, M.443, T.446, N.447, L.449, Y.450, R.453, E.466, K.467, I.469, L.470, I.569, L.572, Q.573, I.576 Chain B: F.483, L.542 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.407, A:L.411, A:L.411, A:L.449, A:E.466, A:I.469, B:L.542 Hydrogen bonds: A:S.406, A:Y.407, A:S.408, A:K.467, A:Q.573 Salt bridges: A:R.453 8IJ.3: 30 residues within 4Å: Chain B: R.305, H.306, F.403, V.404, D.405, S.406, Y.407, S.408, I.410, L.411, F.439, A.442, M.443, T.446, N.447, L.449, Y.450, R.453, E.466, K.467, L.470, I.569, L.572, Q.573, I.576 Chain D: F.483, F.487, L.535, A.538, L.542 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.407, B:I.410, B:A.442, B:L.449, D:L.542 Hydrogen bonds: B:R.305, B:R.305, B:S.406, B:Y.407, B:S.408, B:R.453, B:Q.573 Salt bridges: B:R.453

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

NA.2: 7 residues within 4Å: Chain A: G.516 Chain B: G.516, M.517 Chain C: G.516 Chain D: G.516, M.517 Ligands: NA.5 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.516 NA.5: 6 residues within 4Å: Chain A: G.516 Chain B: G.516 Chain C: G.516 Chain D: I.515, G.516 Ligands: NA.2 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.516

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

NKN.4: 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 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:F.487, A:F.487, A:I.534, C:F.439, C:F.439 Hydrogen bonds: C:S.408, C:S.408, C:T.446 NKN.6: 17 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.418, F.439, A.442, M.443, T.446, N.447, L.449, I.465 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.439, D:F.439, D:F.439, C:F.487 Hydrogen bonds: D:Y.407, D:Y.407

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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