SMTL ID : 8ffn.1

RR-bound wildtype rabbit TRPV5 in nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

R2R.1: 8 residues within 4Å: Chain A: T.539, D.542 Chain B: T.539, D.542 Chain C: T.539, D.542 Chain D: T.539, D.542 12 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B, 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: A:T.539, A:T.539, A:D.542, B:T.539, B:T.539, B:D.542, C:T.539, C:T.539, C:D.542, C:D.542, D:T.539, D:T.539

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

POV.2: 12 residues within 4Å: Chain A: L.502, H.509, Q.513, D.525, Y.526, P.527, L.530 Chain D: I.337, I.341, T.345, I.348, Y.349 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:L.502, A:L.502, A:Y.526, A:P.527, D:I.337, D:I.341, D:I.341, D:I.341, D:T.345 Hydrogen bonds: A:Y.526 POV.3: 15 residues within 4Å: Chain A: R.326, C.330, A.333, S.334, I.337, V.465, F.468, A.469, F.472, Q.473, M.474, L.475 Chain B: W.495, L.496, V.499 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:W.495, B:L.496, B:V.499, A:A.333, A:I.337, A:F.468, A:F.472, A:F.472, A:F.472 Hydrogen bonds: A:Q.473, A:M.474 POV.6: 12 residues within 4Å: Chain A: I.337, I.341, T.345, I.348, Y.349 Chain B: L.502, H.509, Q.513, D.525, Y.526, P.527, L.530 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.337, A:I.341, A:I.341, A:I.341, A:T.345, B:L.502, B:L.502, B:Y.526, B:P.527 Hydrogen bonds: B:Y.526 POV.7: 15 residues within 4Å: Chain B: R.326, C.330, A.333, S.334, I.337, V.465, F.468, A.469, F.472, Q.473, M.474, L.475 Chain C: W.495, L.496, V.499 11 PLIP interactions: 3 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:W.495, C:L.496, C:V.499, B:A.333, B:I.337, B:F.468, B:F.472, B:F.472, B:F.472 Hydrogen bonds: B:Q.473, B:M.474 POV.10: 12 residues within 4Å: Chain B: I.337, I.341, T.345, I.348, Y.349 Chain C: L.502, H.509, Q.513, D.525, Y.526, P.527, L.530 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.502, C:L.502, C:Y.526, C:P.527, B:I.337, B:I.341, B:I.341, B:I.341, B:T.345 Hydrogen bonds: C:Y.526 POV.11: 15 residues within 4Å: Chain C: R.326, C.330, A.333, S.334, I.337, V.465, F.468, A.469, F.472, Q.473, M.474, L.475 Chain D: W.495, L.496, V.499 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:A.333, C:I.337, C:F.468, C:F.472, C:F.472, C:F.472, D:W.495, D:L.496, D:V.499 Hydrogen bonds: C:Q.473, C:M.474 POV.14: 12 residues within 4Å: Chain C: I.337, I.341, T.345, I.348, Y.349 Chain D: L.502, H.509, Q.513, D.525, Y.526, P.527, L.530 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.502, D:L.502, D:Y.526, D:P.527, C:I.337, C:I.341, C:I.341, C:I.341, C:T.345 Hydrogen bonds: D:Y.526 POV.15: 15 residues within 4Å: Chain A: W.495, L.496, V.499 Chain D: R.326, C.330, A.333, S.334, I.337, V.465, F.468, A.469, F.472, Q.473, M.474, L.475 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:A.333, D:I.337, D:F.468, D:F.472, D:F.472, D:F.472, A:W.495, A:L.496, A:V.499 Hydrogen bonds: D:Q.473, D:M.474

8 x ERG: ERGOSTEROL(Non-covalent)

ERG.4: 16 residues within 4Å: Chain A: P.424, F.425, I.428, F.456, V.459, L.460, C.463, T.479, I.482, Q.483, I.486 Chain B: F.504, I.557, T.558, A.561, I.565 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:P.424, A:F.425, A:I.428, A:F.456, A:F.456, A:L.460, A:T.479, A:I.482, A:Q.483, A:I.486, B:F.504, B:I.557, B:A.561, B:I.565, B:I.565 Hydrogen bonds: A:T.479, A:Q.483 ERG.5: 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 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.557, B:A.560, B:I.564, A:A.498, A:P.527, A:F.531, A:F.531 ERG.8: 16 residues within 4Å: Chain B: P.424, F.425, I.428, F.456, V.459, L.460, C.463, T.479, I.482, Q.483, I.486 Chain C: F.504, I.557, T.558, A.561, I.565 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:P.424, B:F.425, B:I.428, B:F.456, B:F.456, B:L.460, B:T.479, B:I.482, B:Q.483, B:I.486, C:F.504, C:I.557, C:A.561, C:I.565, C:I.565 Hydrogen bonds: B:T.479, B:Q.483 ERG.9: 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 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:A.498, B:P.527, B:F.531, B:F.531, C:I.557, C:A.560, C:I.564 ERG.12: 16 residues within 4Å: Chain C: P.424, F.425, I.428, F.456, V.459, L.460, C.463, T.479, I.482, Q.483, I.486 Chain D: F.504, I.557, T.558, A.561, I.565 17 PLIP interactions: 5 interactions with chain D, 12 interactions with chain C Hydrophobic interactions: D:F.504, D:I.557, D:A.561, D:I.565, D:I.565, C:P.424, C:F.425, C:I.428, C:F.456, C:F.456, C:L.460, C:T.479, C:I.482, C:Q.483, C:I.486 Hydrogen bonds: C:T.479, C:Q.483 ERG.13: 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 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:A.498, C:P.527, C:F.531, C:F.531, D:I.557, D:A.560, D:I.564 ERG.16: 16 residues within 4Å: Chain A: F.504, I.557, T.558, A.561, I.565 Chain D: P.424, F.425, I.428, F.456, V.459, L.460, C.463, T.479, I.482, Q.483, I.486 17 PLIP interactions: 5 interactions with chain A, 12 interactions with chain D Hydrophobic interactions: A:F.504, A:I.557, A:A.561, A:I.565, A:I.565, D:P.424, D:F.425, D:I.428, D:F.456, D:F.456, D:L.460, D:T.479, D:I.482, D:Q.483, D:I.486 Hydrogen bonds: D:T.479, D:Q.483 ERG.17: 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 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:I.557, A:A.560, A:I.564, D:A.498, D:P.527, D:F.531, D:F.531

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 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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