SMTL ID : 8tf4.1

Wildtype rabbit TRPV5 into nanodiscs in the presence of PI(4,5)P2 and econazole

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x ERG: ERGOSTEROL(Non-covalent)

ERG.1: 13 residues within 4Å: Chain A: P.424, F.425, I.428, F.456, V.459, L.460, T.479, I.482, Q.483, I.486 Chain D: I.557, A.561, I.565 13 PLIP interactions: 3 interactions with chain D, 10 interactions with chain A Hydrophobic interactions: D:I.557, D:A.561, D:I.565, A:P.424, A:F.425, A:I.428, A:F.456, A:F.456, A:T.479, A:I.482 Hydrogen bonds: A:T.479, A:Q.483, A:Q.483 ERG.2: 12 residues within 4Å: Chain A: C.494, M.497, A.498, I.501, P.527, L.530, F.531, F.534 Chain D: C.556, A.560, I.564 Ligands: CPL.6 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:A.560, D:I.564, A:A.498, A:I.501, A:P.527, A:L.530, A:F.534, A:F.534 ERG.7: 13 residues within 4Å: Chain A: I.557, A.561, I.565 Chain B: P.424, F.425, I.428, F.456, V.459, L.460, T.479, I.482, Q.483, I.486 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.424, B:F.425, B:I.428, B:F.456, B:F.456, B:T.479, B:I.482, A:I.557, A:A.561, A:I.565 Hydrogen bonds: B:T.479, B:Q.483, B:Q.483 ERG.8: 12 residues within 4Å: Chain A: C.556, A.560, I.564 Chain B: C.494, M.497, A.498, I.501, P.527, L.530, F.531, F.534 Ligands: CPL.11 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.498, B:I.501, B:P.527, B:L.530, B:F.534, B:F.534, A:A.560, A:I.564 ERG.12: 13 residues within 4Å: Chain B: I.557, A.561, I.565 Chain C: P.424, F.425, I.428, F.456, V.459, L.460, T.479, I.482, Q.483, I.486 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:P.424, C:F.425, C:I.428, C:F.456, C:F.456, C:T.479, C:I.482, B:I.557, B:A.561, B:I.565 Hydrogen bonds: C:T.479, C:Q.483, C:Q.483 ERG.13: 12 residues within 4Å: Chain B: C.556, A.560, I.564 Chain C: C.494, M.497, A.498, I.501, P.527, L.530, F.531, F.534 Ligands: CPL.16 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.498, C:I.501, C:P.527, C:L.530, C:F.534, C:F.534, B:A.560, B:I.564 ERG.17: 13 residues within 4Å: Chain C: I.557, A.561, I.565 Chain D: P.424, F.425, I.428, F.456, V.459, L.460, T.479, I.482, Q.483, I.486 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:P.424, D:F.425, D:I.428, D:F.456, D:F.456, D:T.479, D:I.482, C:I.557, C:A.561, C:I.565 Hydrogen bonds: D:T.479, D:Q.483, D:Q.483 ERG.18: 12 residues within 4Å: Chain C: C.556, A.560, I.564 Chain D: C.494, M.497, A.498, I.501, P.527, L.530, F.531, F.534 Ligands: CPL.5 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.498, D:I.501, D:P.527, D:L.530, D:F.534, D:F.534, C:A.560, C:I.564

8 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.3: 11 residues within 4Å: Chain A: F.343, C.346, C.347, L.373, Y.377, L.386, E.389, T.392, M.440, R.443, L.444 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.343, A:Y.377, A:Y.377, A:E.389, A:T.392, A:M.440, A:R.443, A:L.444 CPL.5: 18 residues within 4Å: Chain A: I.337, I.341, T.344, T.345, I.348, Y.349 Chain D: C.494, W.495, A.498, V.499, L.502, H.509, D.525, Y.526, P.527, L.530 Ligands: ECN.4, ERG.18 13 PLIP interactions: 8 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:W.495, D:A.498, D:V.499, D:L.502, D:Y.526, D:P.527, D:L.530, A:I.337, A:I.337, A:I.341, A:I.341, A:T.344 Hydrogen bonds: D:Y.526 CPL.6: 18 residues within 4Å: Chain A: C.494, W.495, A.498, V.499, L.502, H.509, D.525, Y.526, P.527, L.530 Chain B: I.337, I.341, T.344, T.345, I.348, Y.349 Ligands: ERG.2, ECN.10 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.495, A:A.498, A:V.499, A:L.502, A:Y.526, A:P.527, A:L.530, B:I.337, B:I.337, B:I.341, B:I.341, B:T.344 Hydrogen bonds: A:Y.526 CPL.9: 11 residues within 4Å: Chain B: F.343, C.346, C.347, L.373, Y.377, L.386, E.389, T.392, M.440, R.443, L.444 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.343, B:Y.377, B:Y.377, B:E.389, B:T.392, B:M.440, B:R.443, B:L.444 CPL.11: 18 residues within 4Å: Chain B: C.494, W.495, A.498, V.499, L.502, H.509, D.525, Y.526, P.527, L.530 Chain C: I.337, I.341, T.344, T.345, I.348, Y.349 Ligands: ERG.8, ECN.15 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:W.495, B:A.498, B:V.499, B:L.502, B:Y.526, B:P.527, B:L.530, C:I.337, C:I.337, C:I.341, C:I.341, C:T.344 Hydrogen bonds: B:Y.526 CPL.14: 11 residues within 4Å: Chain C: F.343, C.346, C.347, L.373, Y.377, L.386, E.389, T.392, M.440, R.443, L.444 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.343, C:Y.377, C:Y.377, C:L.386, C:E.389, C:T.392, C:M.440, C:R.443, C:L.444 CPL.16: 18 residues within 4Å: Chain C: C.494, W.495, A.498, V.499, L.502, H.509, D.525, Y.526, P.527, L.530 Chain D: I.337, I.341, T.344, T.345, I.348, Y.349 Ligands: ERG.13, ECN.20 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:W.495, C:A.498, C:V.499, C:L.502, C:Y.526, C:P.527, C:L.530, D:I.337, D:I.337, D:I.341, D:I.341, D:T.344 Hydrogen bonds: C:Y.526 CPL.19: 11 residues within 4Å: Chain D: F.343, C.346, C.347, L.373, Y.377, L.386, E.389, T.392, M.440, R.443, L.444 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.343, D:Y.377, D:Y.377, D:E.389, D:T.392, D:M.440, D:R.443, D:L.444

4 x ECN: 1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE(Non-covalent)

ECN.4: 12 residues within 4Å: Chain A: S.334, I.337, V.465, M.466, F.468, A.469, F.472, L.475 Chain D: W.495, L.496, V.499 Ligands: CPL.5 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:W.495, D:W.495, A:I.337, A:F.468, A:L.475 ECN.10: 12 residues within 4Å: Chain A: W.495, L.496, V.499 Chain B: S.334, I.337, V.465, M.466, F.468, A.469, F.472, L.475 Ligands: CPL.6 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.495, A:W.495, B:I.337, B:F.468, B:L.475 ECN.15: 12 residues within 4Å: Chain B: W.495, L.496, V.499 Chain C: S.334, I.337, V.465, M.466, F.468, A.469, F.472, L.475 Ligands: CPL.11 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:W.495, B:W.495, C:I.337, C:F.468, C:L.475 ECN.20: 12 residues within 4Å: Chain C: W.495, L.496, V.499 Chain D: S.334, I.337, V.465, M.466, F.468, A.469, F.472, L.475 Ligands: CPL.16 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.337, D:F.468, D:L.475, C:W.495, C:W.495

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Jesus-Perez, J.J. et al., Structural mechanism of TRPV5 inhibition by econazole. Structure (2024)

Release Date

2024-01-10

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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