SMTL ID : 7mzd.1

Cryo-EM structure of minimal TRPV1 with RTX bound in C2 state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 6EU: resiniferatoxin(Non-covalent)

6EU.1: 19 residues within 4Å: Chain A: Y.407, S.408, L.411, F.412, A.442, M.443, T.446, N.447, L.449, Y.450, R.453, E.466, I.469, L.473 Chain B: F.483, F.487, A.538, I.541, L.542 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.407, A:L.411, A:A.442, A:L.449, A:L.449, A:L.473, B:A.538, B:I.541, B:L.542, B:L.542, B:L.542 Hydrogen bonds: A:T.446, A:T.446, A:R.453 pi-Stacking: A:Y.407 6EU.4: 18 residues within 4Å: Chain B: Y.407, S.408, L.411, F.412, A.442, M.443, T.446, N.447, L.449, Y.450, R.453, E.466, I.469, L.473 Chain D: F.483, A.538, I.541, L.542 14 PLIP interactions: 4 interactions with chain D, 10 interactions with chain B Hydrophobic interactions: D:A.538, D:I.541, D:L.542, D:L.542, B:Y.407, B:L.411, B:A.442, B:L.449, B:L.449, B:L.473 Hydrogen bonds: B:T.446, B:T.446, B:R.453 pi-Stacking: B:Y.407 6EU.5: 19 residues within 4Å: Chain A: F.483, F.487, A.538, 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, E.466, I.469, L.473 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:Y.407, C:L.411, C:A.442, C:L.449, C:L.449, C:L.473, A:A.538, A:I.541, A:L.542, A:L.542 Hydrogen bonds: C:T.446, C:T.446, C:R.453 pi-Stacking: C:Y.407 6EU.6: 19 residues within 4Å: Chain C: F.483, F.487, A.538, I.541, L.542 Chain D: Y.407, S.408, L.411, F.412, A.442, M.443, T.446, N.447, L.449, Y.450, R.453, E.466, I.469, L.473 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:Y.407, D:L.411, D:A.442, D:L.449, D:L.449, D:L.473, C:A.538, C:I.541, C:L.542, C:L.542, C:L.542 Hydrogen bonds: D:T.446, D:T.446, D:R.453 pi-Stacking: D:Y.407

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

NA.2: 5 residues within 4Å: Chain A: G.516 Chain B: G.516 Chain C: G.516 Chain D: G.516 Ligands: NA.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.516 NA.3: 2 residues within 4Å: Chain C: G.516 Ligands: NA.2 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: 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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