SMTL ID : 7l2p.1

cryo-EM structure of unliganded minimal TRPV1

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: 18 residues within 4Å: Chain A: R.305, H.306, D.405, S.406, Y.407, S.408, L.411, T.446, L.449, Y.450, R.453, E.466, I.569, L.572, Q.573, I.576 Chain B: F.487, L.542 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.411, A:L.449, B:F.487, B:L.542 Hydrogen bonds: A:R.305, A:R.305, A:H.306, A:S.406, A:Y.407, A:S.408 Salt bridges: A:R.453 XJ7.5: 16 residues within 4Å: Chain B: R.305, H.306, D.405, S.406, Y.407, S.408, L.411, T.446, L.449, Y.450, R.453, E.466, L.572, Q.573, I.576 Chain D: L.542 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.449, D:L.542 Hydrogen bonds: B:H.306, B:S.406, B:Y.407, B:S.408 Salt bridges: B:R.453 XJ7.7: 15 residues within 4Å: Chain A: F.487, L.542 Chain C: D.405, Y.407, S.408, L.411, T.446, L.449, Y.450, R.453, E.466, I.569, L.572, Q.573, I.576 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.411, C:L.449, C:L.449, A:F.487, A:L.542 Hydrogen bonds: C:R.305, C:R.305, C:S.406, C:Y.407, C:S.408 Salt bridges: C:R.453 XJ7.8: 13 residues within 4Å: Chain C: L.542 Chain D: D.405, Y.407, S.408, L.411, T.446, L.449, Y.450, R.453, E.466, L.572, Q.573, I.576 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.542, C:L.542 Hydrogen bonds: D:R.305, D:R.305, D:S.406, D:Y.407, D:S.408 Salt bridges: 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: 13 residues within 4Å: Chain A: M.477, L.481, L.503, Y.504, S.505, C.507, L.508, F.511 Chain B: K.529, I.533, I.534, L.537, I.541 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.533, B:I.534, B:L.537, B:L.537, B:I.541, A:L.481, A:L.503, A:L.503, A:Y.504, A:F.511 Salt bridges: B:K.529 6IY.3: 11 residues within 4Å: Chain A: K.529, I.533, I.534, L.537 Chain C: M.477, L.481, L.484, L.503, Y.504, C.507, F.511 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.481, C:L.484, C:L.503, C:Y.504, C:F.511, C:F.511, A:I.533, A:I.534, A:L.537 Salt bridges: A:K.529 6IY.6: 13 residues within 4Å: Chain B: M.477, L.481, L.484, S.502, L.503, Y.504, S.505, F.511 Chain D: K.529, I.533, I.534, L.537, I.541 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:L.481, B:L.484, B:L.503, B:Y.504, B:F.511, B:F.511, D:I.533, D:I.534, D:L.537, D:I.541 Hydrogen bonds: B:S.502 Salt bridges: D:K.529, D:K.529 6IY.9: 13 residues within 4Å: Chain C: K.529, A.530, I.533, I.534, L.537 Chain D: M.477, L.481, L.484, L.503, Y.504, S.505, C.507, F.511 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.481, D:L.484, D:L.503, D:Y.504, D:F.511, D:F.511, C:A.530, C:I.533, C:I.534, C:L.537 Salt bridges: C:K.529

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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