SMTL ID : 7l2r.1

Cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

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: 10 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.411 Hydrogen bonds: A:R.305, A:Y.407, A:S.408 Salt bridges: A:R.453 XJ7.5: 12 residues within 4Å: Chain D: R.305, D.405, Y.407, S.408, L.411, M.443, T.446, Y.450, R.453, E.466, Q.573, I.576 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.411 Hydrogen bonds: D:R.305, D:Y.407, D:S.408 Salt bridges: D:R.453 XJ7.7: 12 residues within 4Å: Chain E: R.305, D.405, Y.407, S.408, L.411, T.446, L.449, Y.450, R.453, E.466, Q.573, I.576 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:L.411, E:T.446, E:L.449 Hydrogen bonds: E:R.305, E:R.305, E:S.406, E:Y.407, E:S.408, E:R.453 Salt bridges: E:R.453 XJ7.8: 12 residues within 4Å: Chain F: R.305, D.405, Y.407, S.408, L.411, M.443, T.446, Y.450, R.453, E.466, Q.573, I.576 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:L.411, F:T.446 Hydrogen bonds: F:R.305, F:Y.407, F:S.408 Salt bridges: F:R.453

4 x 65I: (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate(Non-covalent)

65I.2: 7 residues within 4Å: Chain A: M.477, Y.504, F.511 Chain C: A.67, F.68 Chain D: Y.349 Chain F: I.541 5 PLIP interactions: 1 interactions with chain F, 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: F:I.541, A:Y.504, A:F.511 Hydrogen bonds: D:Y.349, C:F.68 65I.4: 7 residues within 4Å: Chain B: A.67, F.68 Chain D: I.541 Chain E: M.477, Y.504, F.511 Chain F: Y.349 5 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E, 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: F:Y.349, B:F.68 Hydrophobic interactions: E:Y.504, E:F.511, D:I.541 65I.6: 6 residues within 4Å: Chain A: I.541 Chain B: E.27 Chain D: M.477, S.502, L.503 Chain E: Y.349 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: E:Y.349, B:E.27 Hydrophobic interactions: A:I.541 65I.9: 7 residues within 4Å: Chain A: Y.349 Chain C: E.27, F.28 Chain E: I.541 Chain F: M.477, L.503, F.511 4 PLIP interactions: 1 interactions with chain F, 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: F:F.511, E:I.541 Hydrogen bonds: A:Y.349, A:Y.349

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

NA.3: 4 residues within 4Å: Chain A: G.516 Chain D: G.516 Chain E: G.516 Chain F: G.516 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A: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: ADEF
Tau-theraphotoxin-Hs1a: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

E
C

F
D

B
F

C
E

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily V member 1

Tau-theraphotoxin-Hs1a

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