SMTL ID : 7mze.1

Cryo-EM structure of minimal TRPV1 with 2 bound RTX in opposite pockets

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

2 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: 11 residues within 4Å: Chain A: R.305, D.405, Y.407, S.408, L.411, T.446, R.453, E.466, Q.573, I.576 Chain B: L.542 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.305, A:R.305, A:S.406, A:Y.407, A:S.408, A:K.467 Salt bridges: A:R.453 Hydrophobic interactions: B:L.542 XJ7.5: 12 residues within 4Å: Chain D: R.305, D.405, Y.407, S.408, L.411, M.443, T.446, R.453, E.466, K.467, Q.573, I.576 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.411 Hydrogen bonds: D:R.305, D:R.305, D:S.406, D:Y.407, D:S.408, D:E.466, D:K.467 Salt bridges: D:R.453

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

NA.2: 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

2 x 6EU: resiniferatoxin(Non-covalent)

6EU.3: 13 residues within 4Å: Chain B: Y.407, S.408, L.411, A.442, M.443, T.446, N.447, L.449, Y.450, R.453, E.466 Chain D: F.487, I.541 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:Y.407, B:L.411, B:A.442, B:L.449, D:F.487, D:I.541 Hydrogen bonds: B:S.408, B:R.453 pi-Stacking: B:Y.407 6EU.4: 14 residues within 4Å: Chain A: F.487, A.538, I.541, L.542 Chain C: Y.407, S.408, L.411, A.442, M.443, T.446, N.447, L.449, Y.450, E.466 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.487, A:A.538, A:I.541, A:L.542, C:Y.407, C:L.411, C:A.442, C:L.449 Hydrogen bonds: C:S.408 pi-Stacking: C:Y.407

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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