SMTL ID : 8fhh.1

Wildtype rabbit TRPV5 in nanodiscs in the presence of oleoyl coenzyme A, Closed stated

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 13 residues within 4Å: Chain A: W.495, A.498, V.499, L.502, Q.513, D.525, Y.526, P.527, L.530 Chain D: I.341, T.344, I.348, Y.349 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:W.495, A:A.498, A:V.499, A:L.502, A:L.502, A:L.530, D:I.341, D:I.341, D:T.344 Hydrogen bonds: A:H.509, A:Y.526 pi-Cation interactions: D:Y.349 POV.4: 13 residues within 4Å: Chain A: I.341, T.344, I.348, Y.349 Chain B: W.495, A.498, V.499, L.502, Q.513, D.525, Y.526, P.527, L.530 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.495, B:A.498, B:V.499, B:L.502, B:L.502, B:L.530, A:I.341, A:I.341, A:T.344 Hydrogen bonds: B:H.509, B:Y.526 pi-Cation interactions: A:Y.349 POV.7: 13 residues within 4Å: Chain B: I.341, T.344, I.348, Y.349 Chain C: W.495, A.498, V.499, L.502, Q.513, D.525, Y.526, P.527, L.530 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:W.495, C:A.498, C:V.499, C:L.502, C:L.502, C:L.530, B:I.341, B:I.341, B:T.344 Hydrogen bonds: C:H.509, C:Y.526 pi-Cation interactions: B:Y.349 POV.10: 13 residues within 4Å: Chain C: I.341, T.344, I.348, Y.349 Chain D: W.495, A.498, V.499, L.502, Q.513, D.525, Y.526, P.527, L.530 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:W.495, D:A.498, D:V.499, D:L.502, D:L.502, D:L.530, C:I.341, C:I.341, C:T.344 Hydrogen bonds: D:H.509, D:Y.526 pi-Cation interactions: C:Y.349

8 x ERG: ERGOSTEROL(Non-covalent)

ERG.2: 14 residues within 4Å: Chain A: P.424, F.425, I.428, F.456, V.459, L.460, C.463, M.466, T.479, I.482, Q.483, I.486 Chain B: F.504, A.561 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.424, A:F.425, A:F.425, A:F.456, A:V.459, A:L.460, A:T.479, A:I.482, A:I.486, B:F.504, B:A.561 Hydrogen bonds: A:T.479, A:Q.483 ERG.3: 10 residues within 4Å: Chain A: C.494, M.497, A.498, I.501, P.527, L.530, F.534 Chain B: C.556, I.557, A.560 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.557, B:A.560, A:A.498, A:I.501, A:P.527, A:L.530, A:F.534 ERG.5: 14 residues within 4Å: Chain B: P.424, F.425, I.428, F.456, V.459, L.460, C.463, M.466, T.479, I.482, Q.483, I.486 Chain C: F.504, A.561 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:P.424, B:F.425, B:F.425, B:F.456, B:V.459, B:L.460, B:T.479, B:I.482, B:I.486, C:F.504, C:A.561 Hydrogen bonds: B:T.479, B:Q.483 ERG.6: 10 residues within 4Å: Chain B: C.494, M.497, A.498, I.501, P.527, L.530, F.534 Chain C: C.556, I.557, A.560 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:A.498, B:I.501, B:P.527, B:L.530, B:F.534, C:I.557, C:A.560 ERG.8: 14 residues within 4Å: Chain C: P.424, F.425, I.428, F.456, V.459, L.460, C.463, M.466, T.479, I.482, Q.483, I.486 Chain D: F.504, A.561 13 PLIP interactions: 2 interactions with chain D, 11 interactions with chain C Hydrophobic interactions: D:F.504, D:A.561, C:P.424, C:F.425, C:F.425, C:F.456, C:V.459, C:L.460, C:T.479, C:I.482, C:I.486 Hydrogen bonds: C:T.479, C:Q.483 ERG.9: 10 residues within 4Å: Chain C: C.494, M.497, A.498, I.501, P.527, L.530, F.534 Chain D: C.556, I.557, A.560 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:I.557, D:A.560, C:A.498, C:I.501, C:P.527, C:L.530, C:F.534 ERG.11: 14 residues within 4Å: Chain A: F.504, A.561 Chain D: P.424, F.425, I.428, F.456, V.459, L.460, C.463, M.466, T.479, I.482, Q.483, I.486 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:P.424, D:F.425, D:F.425, D:F.456, D:V.459, D:L.460, D:T.479, D:I.482, D:I.486, A:F.504, A:A.561 Hydrogen bonds: D:T.479, D:Q.483 ERG.12: 10 residues within 4Å: Chain A: C.556, I.557, A.560 Chain D: C.494, M.497, A.498, I.501, P.527, L.530, F.534 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:A.498, D:I.501, D:P.527, D:L.530, D:F.534, A:I.557, A:A.560

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, B.H. et al., Structural basis of the activation of TRPV5 channels by long-chain acyl-Coenzyme-A. Nat Commun (2023)

Release Date

2023-11-01

Peptides

Transient receptor potential cation channel subfamily V member 5: 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 5

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