SMTL ID : 7l2u.1

cryo-EM structure of DkTx-bound minimal TRPV1 in 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: 14 residues within 4Å: Chain A: R.305, V.404, D.405, S.406, Y.407, S.408, L.411, T.446, R.453, E.466, K.467, I.569, L.572, Q.573 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.407, A:T.446 Hydrogen bonds: A:R.305, A:S.406, A:Y.407, A:S.408, A:R.453, A:K.467, A:K.467, A:Q.573 XJ7.7: 13 residues within 4Å: Chain D: R.305, V.404, D.405, S.406, Y.407, S.408, L.411, T.446, R.453, E.466, L.470, Q.573, I.576 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.407, D:Y.407 Hydrogen bonds: D:R.305, D:V.404, D:D.405, D:S.406, D:Y.407, D:S.408, D:R.453, D:Q.573 XJ7.8: 14 residues within 4Å: Chain E: R.305, D.405, S.406, Y.407, S.408, L.411, T.446, R.453, E.466, I.469, L.470, I.569, L.572, Q.573 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:Y.407, E:T.446, E:I.469, E:L.470 Hydrogen bonds: E:R.305, E:S.406, E:Y.407, E:S.408, E:R.453, E:Q.573 Salt bridges: E:R.453 XJ7.10: 13 residues within 4Å: Chain F: V.404, D.405, S.406, Y.407, S.408, L.411, T.446, Y.450, R.453, E.466, L.470, L.572, Q.573 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:Y.407, F:L.470 Hydrogen bonds: F:S.406, F:Y.407, F:S.408, F:Q.573 Salt bridges: F:R.453, F:R.453

4 x XKP: (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate(Non-covalent)

XKP.2: 6 residues within 4Å: Chain A: L.503, Y.504, C.507, F.511 Chain C: A.67, F.68 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.504, A:F.511 Hydrogen bonds: C:F.68 XKP.4: 7 residues within 4Å: Chain B: E.27, F.28 Chain D: L.503, Y.504, C.507, L.508, F.511 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.508, D:F.511 XKP.5: 6 residues within 4Å: Chain B: A.67, F.68, I.69 Chain E: L.503, L.508, F.511 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:L.503, E:L.508, E:F.511, E:F.511 Hydrogen bonds: B:F.68, B:I.69 XKP.6: 4 residues within 4Å: Chain C: E.27, F.28 Chain F: C.507, F.511 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: F:F.511 Hydrogen bonds: C:E.27

2 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 NA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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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