SMTL ID : 7l2s.1

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

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: 10 residues within 4Å: Chain A: R.305, D.405, Y.407, S.408, L.411, Y.450, R.453, E.466, L.572, Q.573 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.305, A:R.305, A:Y.407, A:S.408, A:R.453, A:E.466, A:Q.573 Salt bridges: A:R.453 XJ7.3: 13 residues within 4Å: Chain B: R.305, H.306, D.405, Y.407, S.408, L.411, T.446, R.453, E.466, K.467, L.572, Q.573, I.576 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.407, B:L.411 Hydrogen bonds: B:R.305, B:Y.407, B:S.408, B:E.466, B:K.467, B:K.467, B:Q.573 Salt bridges: B:R.453 XJ7.6: 12 residues within 4Å: Chain C: R.305, D.405, Y.407, S.408, L.411, T.446, L.449, Y.450, R.453, E.466, L.572, Q.573 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.411, C:L.449 Hydrogen bonds: C:R.305, C:Y.407, C:S.408, C:R.453, C:E.466, C:K.467, C:K.467, C:Q.573 Salt bridges: C:R.453 XJ7.9: 13 residues within 4Å: Chain D: R.305, D.405, Y.407, S.408, L.411, L.449, Y.450, R.453, E.466, K.467, L.572, Q.573, I.576 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.449 Hydrogen bonds: D:R.305, D:R.305, D:Y.407, D:S.408, D:E.466, D:K.467, D:Q.573 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: K.529, L.537 Chain B: M.477, Y.504, C.507, F.511 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.537, B:Y.504, B:F.511, B:F.511 Salt bridges: A:K.529 6IY.4: 4 residues within 4Å: Chain B: K.529 Chain C: Y.504, C.507, F.511 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Salt bridges: B:K.529 Hydrophobic interactions: C:Y.504, C:F.511, C:F.511 6IY.7: 4 residues within 4Å: Chain C: K.529, I.534 Chain D: Y.504, F.511 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.534, D:F.511, D:F.511 Salt bridges: C:K.529 6IY.8: 3 residues within 4Å: Chain A: Y.504, F.511 Chain D: K.529 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Salt bridges: D:K.529, D:K.529 Hydrophobic interactions: A:Y.504, A:Y.504, A:F.511, A:F.511

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

NA.5: 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
D

B
A

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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