SMTL ID : 9b3z.1

Rat TRPV2 E724A/D725A bound to probenecid 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: 13 residues within 4Å: Chain A: N.396, C.399, Y.400, V.402, Y.403, Y.447, L.448, Q.452, E.473, F.476, Y.514, Y.515, Y.675 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.402, A:L.448, A:Y.675 Hydrogen bonds: A:N.396, A:Y.447, A:E.473, A:Y.515 PEX.4: 13 residues within 4Å: Chain B: N.396, C.399, Y.400, V.402, Y.403, Y.447, L.448, Q.452, E.473, F.476, Y.514, Y.515, Y.675 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.402, B:L.448, B:Y.675 Hydrogen bonds: B:N.396, B:Y.447, B:E.473, B:Y.515 PEX.7: 13 residues within 4Å: Chain C: N.396, C.399, Y.400, V.402, Y.403, Y.447, L.448, Q.452, E.473, F.476, Y.514, Y.515, Y.675 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.402, C:L.448, C:Y.675 Hydrogen bonds: C:N.396, C:Y.447, C:E.473, C:Y.515 PEX.10: 13 residues within 4Å: Chain D: N.396, C.399, Y.400, V.402, Y.403, Y.447, L.448, Q.452, E.473, F.476, Y.514, Y.515, Y.675 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.402, D:L.448, D:Y.675 Hydrogen bonds: D:N.396, D:Y.447, D:E.473, D:Y.515

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

FZ4.2: 5 residues within 4Å: Chain A: H.521, T.522, Y.525 Chain B: R.539, V.543 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:R.539, B:V.543, A:H.521, A:T.522, A:Y.525 Hydrogen bonds: A:H.521 pi-Stacking: A:H.521 FZ4.5: 5 residues within 4Å: Chain B: H.521, T.522, Y.525 Chain C: R.539, V.543 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:H.521, B:T.522, B:Y.525, C:R.539, C:V.543 Hydrogen bonds: B:H.521 pi-Stacking: B:H.521 FZ4.8: 5 residues within 4Å: Chain C: H.521, T.522, Y.525 Chain D: R.539, V.543 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:H.521, C:T.522, C:Y.525, D:R.539, D:V.543 Hydrogen bonds: C:H.521 pi-Stacking: C:H.521 FZ4.11: 5 residues within 4Å: Chain A: R.539, V.543 Chain D: H.521, T.522, Y.525 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:R.539, A:V.543, D:H.521, D:T.522, D:Y.525 Hydrogen bonds: D:H.521 pi-Stacking: D:H.521

4 x RTO: 4-(dipropylsulfamoyl)benzoic acid(Non-covalent)

RTO.3: 10 residues within 4Å: Chain A: K.118, L.126, Y.162, H.165, K.174, F.198 Chain D: E.332, W.333, C.334, Y.335 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:W.333, D:W.333, D:Y.335, A:L.126, A:Y.162, A:Y.162, A:F.198 Hydrogen bonds: D:C.334, D:C.334, A:K.118 Salt bridges: A:K.174 RTO.6: 10 residues within 4Å: Chain A: E.332, W.333, C.334, Y.335 Chain B: K.118, L.126, Y.162, H.165, K.174, F.198 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:W.333, A:W.333, A:Y.335, B:L.126, B:Y.162, B:Y.162, B:F.198 Hydrogen bonds: A:C.334, A:C.334, B:K.118 Salt bridges: B:K.174 RTO.9: 10 residues within 4Å: Chain B: E.332, W.333, C.334, Y.335 Chain C: K.118, L.126, Y.162, H.165, K.174, F.198 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.126, C:Y.162, C:Y.162, C:F.198, B:W.333, B:W.333, B:Y.335 Hydrogen bonds: C:K.118, B:C.334, B:C.334 Salt bridges: C:K.174 RTO.12: 10 residues within 4Å: Chain C: E.332, W.333, C.334, Y.335 Chain D: K.118, L.126, Y.162, H.165, K.174, F.198 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.126, D:Y.162, D:Y.162, D:F.198, C:W.333, C:W.333, C:Y.335 Hydrogen bonds: D:K.118, C:C.334, C:C.334 Salt bridges: D:K.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rocereta, J.A. et al., Structural insights into TRPV2 modulation by probenecid. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-02-12

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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