SMTL ID : 8fhi.1

Wildtype rabbit TRPV5 in nanodiscs in complex with oleoyl coenzyme A, Open stated

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x ERG: ERGOSTEROL(Non-covalent)

ERG.1: 18 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, F.487 Chain B: F.504, I.557, A.561, I.565 Ligands: 3VV.3 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.424, A:P.424, A:F.425, A:F.425, A:I.428, A:F.456, A:F.456, A:V.459, A:L.460, A:I.482, A:I.486, A:F.487, B:F.504, B:I.557, B:A.561, B:I.565 Hydrogen bonds: A:T.479 ERG.2: 9 residues within 4Å: Chain A: C.494, M.497, A.498, P.527, F.531 Chain B: C.556, I.557, A.560, I.564 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.557, B:A.560, B:I.564, A:A.498, A:F.531 ERG.5: 18 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, F.487 Chain C: F.504, I.557, A.561, I.565 Ligands: 3VV.7 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:P.424, B:P.424, B:F.425, B:F.425, B:I.428, B:F.456, B:F.456, B:V.459, B:L.460, B:I.482, B:I.486, B:F.487, C:F.504, C:I.557, C:A.561, C:I.565 Hydrogen bonds: B:T.479 ERG.6: 9 residues within 4Å: Chain B: C.494, M.497, A.498, P.527, F.531 Chain C: C.556, I.557, A.560, I.564 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.557, C:A.560, C:I.564, B:A.498, B:F.531 ERG.9: 18 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, F.487 Chain D: F.504, I.557, A.561, I.565 Ligands: 3VV.11 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:P.424, C:P.424, C:F.425, C:F.425, C:I.428, C:F.456, C:F.456, C:V.459, C:L.460, C:I.482, C:I.486, C:F.487, D:F.504, D:I.557, D:A.561, D:I.565 Hydrogen bonds: C:T.479 ERG.10: 9 residues within 4Å: Chain C: C.494, M.497, A.498, P.527, F.531 Chain D: C.556, I.557, A.560, I.564 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:A.498, C:F.531, D:I.557, D:A.560, D:I.564 ERG.14: 18 residues within 4Å: Chain A: F.504, I.557, A.561, I.565 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, F.487 Ligands: 3VV.16 17 PLIP interactions: 4 interactions with chain A, 13 interactions with chain D Hydrophobic interactions: A:F.504, A:I.557, A:A.561, A:I.565, D:P.424, D:P.424, D:F.425, D:F.425, D:I.428, D:F.456, D:F.456, D:V.459, D:L.460, D:I.482, D:I.486, D:F.487 Hydrogen bonds: D:T.479 ERG.15: 9 residues within 4Å: Chain A: C.556, I.557, A.560, I.564 Chain D: C.494, M.497, A.498, P.527, F.531 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:A.498, D:F.531, A:I.557, A:A.560, A:I.564

4 x 3VV: S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)(Non-covalent)

3VV.3: 14 residues within 4Å: Chain A: F.416, G.417, T.419, P.424, V.427, I.428, Q.483, K.484, F.487, G.488, D.489, T.581, R.584 Ligands: ERG.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.427 Hydrogen bonds: A:G.417, A:Q.483, A:K.484 Salt bridges: A:K.484, A:R.584 3VV.7: 14 residues within 4Å: Chain B: F.416, G.417, T.419, P.424, V.427, I.428, Q.483, K.484, F.487, G.488, D.489, T.581, R.584 Ligands: ERG.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.427 Hydrogen bonds: B:G.417, B:Q.483, B:K.484 Salt bridges: B:K.484, B:R.584 3VV.11: 14 residues within 4Å: Chain C: F.416, G.417, T.419, P.424, V.427, I.428, Q.483, K.484, F.487, G.488, D.489, T.581, R.584 Ligands: ERG.9 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.427 Hydrogen bonds: C:G.417, C:Q.483, C:K.484 Salt bridges: C:K.484, C:R.584 3VV.16: 14 residues within 4Å: Chain D: F.416, G.417, T.419, P.424, V.427, I.428, Q.483, K.484, F.487, G.488, D.489, T.581, R.584 Ligands: ERG.14 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.427 Hydrogen bonds: D:G.417, D:Q.483, D:K.484 Salt bridges: D:K.484, D:R.584

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

POV.4: 11 residues within 4Å: Chain A: I.337, I.341, T.345, I.348, Y.349 Chain B: W.495, V.499, L.502, Y.526, P.527, L.530 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.499, B:L.502, B:Y.526, B:Y.526, B:L.530, A:I.337, A:I.341 Hydrogen bonds: B:Y.526 pi-Cation interactions: A:Y.349 POV.8: 12 residues within 4Å: Chain B: I.337, I.341, T.344, T.345, I.348, Y.349 Chain C: W.495, V.499, L.502, Y.526, P.527, L.530 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:I.337, B:I.341, B:T.344, C:V.499, C:L.502, C:Y.526, C:Y.526, C:L.530 pi-Cation interactions: B:Y.349 Hydrogen bonds: C:Y.526 POV.12: 11 residues within 4Å: Chain C: I.337, I.341, T.345, I.348, Y.349 Chain D: W.495, V.499, L.502, Y.526, P.527, L.530 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:I.337, C:I.341, D:V.499, D:L.502, D:Y.526, D:Y.526, D:L.530 pi-Cation interactions: C:Y.349 Hydrogen bonds: D:Y.526 POV.13: 11 residues within 4Å: Chain A: W.495, V.499, L.502, Y.526, P.527, L.530 Chain D: I.337, I.341, T.345, I.348, Y.349 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:V.499, A:L.502, A:Y.526, A:Y.526, A:L.530, D:I.337, D:I.341 Hydrogen bonds: A:Y.526 pi-Cation interactions: D:Y.349

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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