SMTL ID : 8ffm.1

Wildtype rat TRPV2 in nanodiscs bound to RR and 2-APB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x PEX: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

PEX.1: 14 residues within 4Å: Chain A: F.395, N.396, C.399, Y.400, V.402, Y.403, Y.447, L.448, Q.452, E.473, Y.514, Y.515, Y.675, W.677 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.395, A:V.402, A:Y.447, A:W.677, A:W.677 Hydrogen bonds: A:N.396, A:Y.447, A:E.473, A:Y.515 PEX.4: 14 residues within 4Å: Chain B: F.395, N.396, C.399, Y.400, V.402, Y.403, Y.447, L.448, Q.452, E.473, Y.514, Y.515, Y.675, W.677 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.395, B:V.402, B:Y.447, B:W.677, B:W.677 Hydrogen bonds: B:N.396, B:Y.447, B:E.473, B:Y.515 PEX.6: 14 residues within 4Å: Chain C: F.395, N.396, C.399, Y.400, V.402, Y.403, Y.447, L.448, Q.452, E.473, Y.514, Y.515, Y.675, W.677 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.395, C:V.402, C:Y.447, C:W.677, C:W.677 Hydrogen bonds: C:N.396, C:Y.447, C:E.473, C:Y.515 PEX.8: 14 residues within 4Å: Chain D: F.395, N.396, C.399, Y.400, V.402, Y.403, Y.447, L.448, Q.452, E.473, Y.514, Y.515, Y.675, W.677 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.395, D:V.402, D:Y.447, D:W.677, D:W.677 Hydrogen bonds: D:N.396, D:Y.447, D:E.473, D:Y.515

4 x FZ4: 2-aminoethyl diphenylborinate(Non-covalent)

FZ4.2: 4 residues within 4Å: Chain A: H.521, T.522, Y.525 Chain B: V.543 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.522, A:Y.525, B:V.543 pi-Stacking: A:H.521, A:Y.525 FZ4.5: 4 residues within 4Å: Chain B: H.521, T.522, Y.525 Chain C: V.543 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.522, B:Y.525, C:V.543 pi-Stacking: B:H.521, B:Y.525 FZ4.7: 4 residues within 4Å: Chain C: H.521, T.522, Y.525 Chain D: V.543 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:V.543, C:T.522, C:Y.525 pi-Stacking: C:H.521, C:Y.525 FZ4.9: 4 residues within 4Å: Chain A: V.543 Chain D: H.521, T.522, Y.525 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:T.522, D:Y.525, A:V.543 pi-Stacking: D:H.521, D:Y.525

1 x R2R: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)(Non-covalent)

R2R.3: 5 residues within 4Å: Chain A: G.606 Chain B: G.606 Chain C: G.606, M.607 Chain D: G.606 8 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: A:G.606, A:G.606, D:G.606, B:G.606, B:G.606, C:G.606, C:G.606, C:G.606

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pumroy, R.A. et al., Molecular details of ruthenium red pore block in TRPV channels. Embo Rep. (2024)

Release Date

2024-02-07

Peptides

Transient receptor potential cation channel subfamily V member 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily V member 2

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