SMTL ID : 7l2w.1

cryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state a

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 6EU: resiniferatoxin(Non-covalent)

6EU.1: 17 residues within 4Å: Chain A: Y.407, S.408, L.411, M.443, T.446, N.447, L.449, Y.450, R.453, A.462, I.465, I.469, L.473 Chain B: F.483, F.487, I.541, L.542 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.411, A:L.411, A:L.473, B:F.487, B:I.541, B:L.542 Hydrogen bonds: A:S.408, A:T.446, A:R.453 pi-Stacking: A:Y.407 6EU.4: 19 residues within 4Å: Chain A: F.483, F.487, I.541, L.542 Chain C: Y.407, S.408, L.411, F.412, A.442, M.443, T.446, N.447, L.449, Y.450, R.453, A.462, I.465, I.469, L.473 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:F.487, A:I.541, A:L.542, A:L.542, C:L.411, C:L.411, C:A.442, C:L.473 Hydrogen bonds: C:S.408, C:T.446, C:R.453 pi-Stacking: C:Y.407 6EU.6: 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, I.465, I.469, L.473 Chain D: F.483, F.487, I.541, L.542 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:F.487, D:I.541, D:L.542, B:L.411, B:L.411, B:L.473 Hydrogen bonds: B:T.446, B:R.453 pi-Stacking: B:Y.407 6EU.8: 17 residues within 4Å: Chain C: F.483, F.487, I.541, L.542 Chain D: Y.407, S.408, L.411, M.443, T.446, N.447, L.449, Y.450, R.453, A.462, I.465, I.469, L.473 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.411, D:L.411, D:I.469, D:I.469, D:L.473, C:F.487, C:I.541, C:L.542 Hydrogen bonds: D:S.408, D:T.446, D:R.453 pi-Stacking: D:Y.407

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: 5 residues within 4Å: Chain A: Y.504 Chain B: K.529, I.533, I.534, I.541 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.541, A:Y.504 Salt bridges: B:K.529 6IY.3: 7 residues within 4Å: Chain A: A.530, I.533, I.534, L.537 Chain C: Y.504, L.508, F.511 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.534, C:L.508, C:F.511 6IY.7: 3 residues within 4Å: Chain B: Y.504 Chain D: A.530, I.534 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:I.534, B:Y.504 Salt bridges: D:K.529 6IY.9: 5 residues within 4Å: Chain C: A.530, I.533, I.534 Chain D: L.473, Y.504 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.473, D:Y.504, C:I.534

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
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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