SMTL ID : 7mza.1

Cryo-EM structure of minimal TRPV1 with 2 bound RTX in adjacent 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: 15 residues within 4Å: Chain A: R.305, D.405, S.406, Y.407, S.408, E.409, L.411, M.443, T.446, Y.450, R.453, E.466, Q.573, I.576 Chain B: L.542 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.407, B:L.542 Hydrogen bonds: A:R.305, A:R.305, A:S.406, A:Y.407, A:S.408, A:Q.573 Salt bridges: A:R.453 XJ7.3: 15 residues within 4Å: Chain C: R.305, D.405, Y.407, S.408, L.411, M.443, T.446, L.449, Y.450, R.453, E.466, K.467, I.569, Q.573, I.576 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.407, C:L.449 Hydrogen bonds: C:R.305, C:R.305, C:Y.407, C:S.408, C:K.467 Salt bridges: C:R.453

2 x 6EU: resiniferatoxin(Non-covalent)

6EU.2: 18 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, A.462, E.466, I.469, L.473 Chain D: F.487, A.538, I.541, L.542 11 PLIP interactions: 4 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: D:F.487, D:A.538, D:I.541, D:L.542, B:Y.407, B:L.411, B:A.442, B:L.449, B:L.473 Hydrogen bonds: B:S.408 pi-Stacking: B:Y.407 6EU.5: 13 residues within 4Å: Chain C: F.487, I.541 Chain D: Y.407, S.408, L.411, F.412, M.443, T.446, N.447, L.449, Y.450, E.466, L.473 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.407, D:L.411, D:L.449, D:L.473, C:I.541 Hydrogen bonds: D:Y.407, D:S.408 pi-Stacking: D:Y.407

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

NA.4: 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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