SMTL ID : 7mz5.1

Cryo-EM structure of RTX-bound full-length TRPV1 in C2 state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 6EU: resiniferatoxin(Non-covalent)

6EU.1: 21 residues within 4Å: Chain A: Y.515, S.516, L.519, F.520, A.550, M.551, T.554, N.555, L.557, Y.558, R.561, A.570, I.573, E.574, I.577, L.581 Chain C: F.591, F.595, A.669, I.672, L.673 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.519, A:L.519, A:L.557, A:L.557, A:A.570, A:L.581, C:F.595, C:A.669, C:I.672, C:L.673 Hydrogen bonds: A:Y.515, A:T.554, A:T.554, A:R.561 pi-Stacking: A:Y.515 6EU.5: 22 residues within 4Å: Chain B: F.511, Y.515, S.516, L.519, F.520, A.550, M.551, T.554, N.555, L.557, Y.558, R.561, A.570, I.573, E.574, I.577, L.581 Chain D: F.591, F.595, A.669, I.672, L.673 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:F.511, B:L.519, B:L.519, B:L.557, B:L.557, B:A.570, B:I.577, B:L.581, D:F.591, D:F.595, D:A.669, D:I.672, D:L.673 Hydrogen bonds: B:Y.515, B:S.516, B:T.554, B:T.554, B:R.561 pi-Stacking: B:Y.515 6EU.6: 21 residues within 4Å: Chain B: F.591, F.595, A.669, I.672, L.673 Chain C: Y.515, S.516, L.519, F.520, A.550, M.551, T.554, N.555, L.557, Y.558, R.561, A.570, I.573, E.574, I.577, L.581 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.519, C:L.519, C:L.557, C:L.557, C:L.581, B:F.595, B:A.669, B:I.672, B:L.673 Hydrogen bonds: C:Y.515, C:T.554, C:T.554, C:R.561 pi-Stacking: C:Y.515 6EU.7: 21 residues within 4Å: Chain A: F.591, F.595, A.669, I.672, L.673 Chain D: Y.515, S.516, L.519, F.520, A.550, M.551, T.554, N.555, L.557, Y.558, R.561, A.570, I.573, E.574, I.577, L.581 17 PLIP interactions: 11 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:L.519, D:L.519, D:L.557, D:L.557, D:I.577, D:L.581, A:F.591, A:F.595, A:A.669, A:I.672, A:L.673, A:L.673 Hydrogen bonds: D:Y.515, D:T.554, D:T.554, D:R.561 pi-Stacking: D:Y.515

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

NA.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.4: 4 residues within 4Å: Chain A: M.686 Chain B: M.686 Chain C: M.686 Chain D: M.686 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
C

C
D

D
B

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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