SMTL ID : 9b3u.1

Rat TRPV2 WT bound to probenecid

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, G.444, Y.447, L.448, Q.452, E.473, F.476, Y.514, Y.515, Y.675, W.677 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.395, A:Y.447, A:Y.447, 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, G.444, Y.447, L.448, Q.452, E.473, F.476, Y.514, Y.515, Y.675, W.677 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.395, B:Y.447, B:Y.447, 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, G.444, Y.447, L.448, Q.452, E.473, F.476, Y.514, Y.515, Y.675, W.677 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.395, C:Y.447, C:Y.447, 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, G.444, Y.447, L.448, Q.452, E.473, F.476, Y.514, Y.515, Y.675, W.677 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.395, D:Y.447, D:Y.447, D:W.677 Hydrogen bonds: D:N.396, D:Y.447, D:E.473, D:Y.515

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

RTO.2: 11 residues within 4Å: Chain A: K.118, L.126, Y.162, H.165, I.170, K.174, F.198, F.199 Chain D: W.333, C.334, Y.335 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:L.126, A:L.126, A:Y.162, A:Y.162, A:F.198, A:F.199, D:W.333, D:Y.335 Salt bridges: A:K.174 Hydrogen bonds: D:C.334 RTO.3: 11 residues within 4Å: Chain A: W.333, C.334, Y.335 Chain B: K.118, L.126, Y.162, H.165, I.170, K.174, F.198, F.199 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.126, B:L.126, B:Y.162, B:Y.162, B:F.198, B:F.199, A:W.333, A:Y.335 Salt bridges: B:K.174 Hydrogen bonds: A:C.334 RTO.5: 11 residues within 4Å: Chain B: W.333, C.334, Y.335 Chain C: K.118, L.126, Y.162, H.165, I.170, K.174, F.198, F.199 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.126, C:L.126, C:Y.162, C:Y.162, C:F.198, C:F.199, B:W.333, B:Y.335 Salt bridges: C:K.174 Hydrogen bonds: B:C.334 RTO.7: 11 residues within 4Å: Chain C: W.333, C.334, Y.335 Chain D: K.118, L.126, Y.162, H.165, I.170, K.174, F.198, F.199 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:W.333, C:Y.335, D:L.126, D:L.126, D:Y.162, D:Y.162, D:F.198, D:F.199 Hydrogen bonds: 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

2025-02-26

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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