SMTL ID : 7mz6.1

Cryo-EM structure of minimal TRPV1 with 1 perturbed PI

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x XJ7: (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate(Non-covalent)

XJ7.1: 12 residues within 4Å: Chain A: R.305, D.405, Y.407, S.408, L.411, T.446, L.449, Y.450, R.453, E.466, Q.573, I.576 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.411, A:L.411, A:L.449 Hydrogen bonds: A:R.305, A:R.305, A:Y.407, A:S.408 Salt bridges: A:R.453 XJ7.4: 14 residues within 4Å: Chain B: R.305, D.405, S.406, Y.407, S.408, L.411, T.446, Y.450, R.453, E.466, I.569, Q.573, I.576 Chain D: L.542 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.411, D:L.542 Hydrogen bonds: B:R.305, B:R.305, B:Y.407, B:S.408 Salt bridges: B:R.453 XJ7.6: 13 residues within 4Å: Chain A: L.542 Chain C: R.305, D.405, S.406, Y.407, S.408, L.411, T.446, L.449, R.453, E.466, Q.573, I.576 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:L.542, C:L.411, C:L.449 Hydrogen bonds: C:R.305, C:R.305, C:Y.407, C:S.408, C:S.408, C:E.466, C:Q.573 Salt bridges: C:R.453 XJ7.7: 12 residues within 4Å: Chain D: R.305, D.405, Y.407, S.408, L.411, T.446, R.453, E.466, K.467, I.569, Q.573, I.576 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.305, D:R.305, D:Y.407, D:S.408, D:E.466, D:K.467 Salt bridges: D:R.453, D:R.453

4 x 6IY: (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate(Non-covalent)

6IY.2: 6 residues within 4Å: Chain A: L.481, L.484, Y.504, S.505, F.511 Chain B: L.537 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.537, A:L.481, A:L.484, A:Y.504, A:Y.504, A:F.511, A:F.511 6IY.3: 9 residues within 4Å: Chain A: K.529, I.533 Chain C: L.481, L.484, L.503, Y.504, C.507, L.508, F.511 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.481, C:L.484, C:L.503, C:Y.504, C:F.511, C:F.511, A:I.533 Salt bridges: A:K.529 6IY.5: 12 residues within 4Å: Chain B: M.477, L.481, L.484, Y.504, S.505, L.508, F.511 Chain D: K.529, A.530, I.533, I.534, L.537 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:A.530, D:I.533, D:I.534, D:L.537, B:L.481, B:L.484, B:Y.504, B:F.511, B:F.511 Salt bridges: D:K.529 6IY.8: 9 residues within 4Å: Chain C: K.529, A.530, I.533 Chain D: L.484, Y.504, S.505, C.507, L.508, F.511 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:I.533, D:L.484, D:Y.504, D:Y.504, D:F.511 Salt bridges: C:K.529 Hydrogen bonds: D:S.502

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

NA.9: 4 residues within 4Å: Chain A: G.516 Chain B: G.516 Chain C: G.516 Chain D: G.516 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.516

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, K. et al., Structural snapshots of TRPV1 reveal mechanism of polymodal functionality. Cell (2021)

Release Date

2021-09-22

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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