SMTL ID : 7l2v.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 6EU: resiniferatoxin(Non-covalent)

6EU.1: 15 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, E.466, I.469 Chain B: F.487, I.541 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.411, A:L.411, A:L.449, B:F.487, B:I.541 Hydrogen bonds: A:S.408, A:R.453 pi-Stacking: A:Y.407 6EU.2: 15 residues within 4Å: Chain B: Y.407, S.408, L.411, M.443, T.446, N.447, L.449, Y.450, R.453, A.462, I.469 Chain D: F.483, F.487, I.541, L.542 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:Y.407, B:L.449, D:F.487, D:I.541, D:L.542 Hydrogen bonds: B:S.408, B:R.453 6EU.3: 16 residues within 4Å: Chain A: F.483, F.487, I.541, L.542 Chain C: Y.407, S.408, L.411, M.443, T.446, N.447, L.449, Y.450, R.453, A.462, I.465, I.469 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.411, C:L.411, C:A.462, C:I.469, A:I.541, A:L.542 Hydrogen bonds: C:S.408, C:T.446, C:R.453 pi-Stacking: C:Y.407 6EU.6: 14 residues within 4Å: Chain C: 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 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.407, D:L.411, D:T.446, D:L.449, C:I.541, C:L.542 Hydrogen bonds: D:S.408, D:R.453

1 x XPS: 6-deoxy-6-(methylamino)-D-galactitol(Non-covalent)

XPS.4: 5 residues within 4Å: Chain B: G.516, G.518 Chain C: G.518 Chain D: G.518 Ligands: NA.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.518

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

NA.5: 2 residues within 4Å: Chain D: G.516 Ligands: XPS.4 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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