SMTL ID : 7s8c.1

Cryo-EM structure of human TRPV6 in complex with inhibitor econazole

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ECL: 1-[(2R)-2-[(4-chlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole(Non-covalent)

ECL.1: 11 residues within 4Å: Chain A: V.465, M.466, F.468, A.469, F.472, M.474, L.475 Chain B: W.495, L.496, V.499 Ligands: POV.16 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.469, A:F.472, A:L.475, B:W.495, B:W.495 ECL.11: 11 residues within 4Å: Chain B: V.465, M.466, F.468, A.469, F.472, M.474, L.475 Chain C: W.495, L.496, V.499 Ligands: POV.24 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:A.469, B:F.472, B:L.475, C:W.495, C:W.495 ECL.19: 11 residues within 4Å: Chain C: V.465, M.466, F.468, A.469, F.472, M.474, L.475 Chain D: W.495, L.496, V.499 Ligands: POV.33 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:W.495, D:W.495, C:A.469, C:F.472, C:L.475 ECL.28: 11 residues within 4Å: Chain A: W.495, L.496, V.499 Chain D: V.465, M.466, F.468, A.469, F.472, M.474, L.475 Ligands: POV.6 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:A.469, D:F.472, D:L.475, A:W.495, A:W.495

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 18 residues within 4Å: Chain A: L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, I.429, Y.467, R.470, M.603 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.332, A:L.332, A:I.335, A:Y.336, A:Y.339, A:Y.339, A:V.391, A:I.394, A:I.398, A:I.399, A:V.402, A:F.425, A:I.429, A:Y.467, A:Y.467 Hydrogen bonds: A:F.425 Salt bridges: A:H.426, A:H.426, A:R.470 Y01.3: 20 residues within 4Å: Chain A: P.424, F.425, L.428, S.455, F.456, V.459, L.460, C.463, R.470, T.479, I.480, I.482, Q.483, I.486, Q.596 Chain B: M.554, I.557, T.558, A.561, I.565 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.424, A:F.425, A:L.428, A:F.456, A:F.456, A:V.459, A:V.459, A:I.482, A:Q.483, A:I.486, B:I.557, B:A.561, B:I.565 Hydrogen bonds: A:T.479, A:Q.596 Salt bridges: A:R.470 Y01.4: 11 residues within 4Å: Chain A: C.494, M.497, P.527, M.528, L.530, F.531, F.534 Chain B: S.556, A.560, I.564 Ligands: POV.6 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.560, B:I.564, A:L.530, A:F.531, A:F.531, A:F.534, A:F.534 Y01.12: 18 residues within 4Å: Chain B: L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, I.429, Y.467, R.470, M.603 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.332, B:L.332, B:I.335, B:Y.336, B:Y.339, B:Y.339, B:V.391, B:I.394, B:I.398, B:I.399, B:V.402, B:F.425, B:I.429, B:Y.467, B:Y.467 Hydrogen bonds: B:F.425 Salt bridges: B:H.426, B:H.426, B:R.470 Y01.13: 20 residues within 4Å: Chain B: P.424, F.425, L.428, S.455, F.456, V.459, L.460, C.463, R.470, T.479, I.480, I.482, Q.483, I.486, Q.596 Chain C: M.554, I.557, T.558, A.561, I.565 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.425, B:L.428, B:F.456, B:F.456, B:V.459, B:V.459, B:I.482, B:Q.483, B:I.486, C:I.557, C:A.561, C:I.565 Hydrogen bonds: B:T.479, B:Q.596 Salt bridges: B:R.470 Y01.14: 11 residues within 4Å: Chain B: C.494, M.497, P.527, M.528, L.530, F.531, F.534 Chain C: S.556, A.560, I.564 Ligands: POV.16 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:A.560, C:I.564, B:L.530, B:F.531, B:F.531, B:F.534, B:F.534 Y01.20: 18 residues within 4Å: Chain C: L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, I.429, Y.467, R.470, M.603 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:L.332, C:L.332, C:I.335, C:Y.336, C:Y.339, C:Y.339, C:V.391, C:I.394, C:I.398, C:I.399, C:V.402, C:F.425, C:I.429, C:Y.467, C:Y.467 Hydrogen bonds: C:F.425 Salt bridges: C:H.426, C:H.426, C:R.470 Y01.21: 20 residues within 4Å: Chain C: P.424, F.425, L.428, S.455, F.456, V.459, L.460, C.463, R.470, T.479, I.480, I.482, Q.483, I.486, Q.596 Chain D: M.554, I.557, T.558, A.561, I.565 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:P.424, C:F.425, C:L.428, C:F.456, C:F.456, C:V.459, C:V.459, C:I.482, C:Q.483, C:I.486, D:I.557, D:A.561, D:I.565 Hydrogen bonds: C:T.479, C:Q.596 Salt bridges: C:R.470 Y01.22: 11 residues within 4Å: Chain C: C.494, M.497, P.527, M.528, L.530, F.531, F.534 Chain D: S.556, A.560, I.564 Ligands: POV.24 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:A.560, D:I.564, C:L.530, C:F.531, C:F.531, C:F.534, C:F.534 Y01.29: 18 residues within 4Å: Chain D: L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, I.429, Y.467, R.470, M.603 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:L.332, D:L.332, D:I.335, D:Y.336, D:Y.339, D:Y.339, D:V.391, D:I.394, D:I.398, D:I.399, D:V.402, D:F.425, D:I.429, D:Y.467, D:Y.467 Hydrogen bonds: D:F.425 Salt bridges: D:H.426, D:H.426, D:R.470 Y01.30: 20 residues within 4Å: Chain A: M.554, I.557, T.558, A.561, I.565 Chain D: P.424, F.425, L.428, S.455, F.456, V.459, L.460, C.463, R.470, T.479, I.480, I.482, Q.483, I.486, Q.596 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:P.424, D:F.425, D:L.428, D:F.456, D:F.456, D:V.459, D:V.459, D:I.482, D:Q.483, D:I.486, A:I.557, A:A.561, A:I.565 Hydrogen bonds: D:T.479, D:Q.596 Salt bridges: D:R.470 Y01.31: 11 residues within 4Å: Chain A: S.556, A.560, I.564 Chain D: C.494, M.497, P.527, M.528, L.530, F.531, F.534 Ligands: POV.33 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.530, D:F.531, D:F.531, D:F.534, D:F.534, A:A.560, A:I.564

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

POV.5: 6 residues within 4Å: Chain A: M.435, M.442, G.449, V.452, P.453 Chain B: F.553 Ligand excluded by PLIP POV.6: 18 residues within 4Å: Chain A: C.494, W.495, A.498, V.499, L.502, Y.509, D.525, Y.526, P.527, L.530 Chain D: I.341, M.345, I.348, Y.349, W.462, V.465 Ligands: Y01.4, ECL.28 Ligand excluded by PLIP POV.7: 11 residues within 4Å: Chain A: C.346, C.347, L.373, Y.377, L.386, E.389, V.393, T.439, R.443, L.444, M.454 Ligand excluded by PLIP POV.8: 8 residues within 4Å: Chain A: C.342, M.345, C.346, Y.349, K.381, I.384, R.385, G.388 Ligand excluded by PLIP POV.15: 6 residues within 4Å: Chain B: M.435, M.442, G.449, V.452, P.453 Chain C: F.553 Ligand excluded by PLIP POV.16: 18 residues within 4Å: Chain A: I.341, M.345, I.348, Y.349, W.462, V.465 Chain B: C.494, W.495, A.498, V.499, L.502, Y.509, D.525, Y.526, P.527, L.530 Ligands: ECL.1, Y01.14 Ligand excluded by PLIP POV.17: 11 residues within 4Å: Chain B: C.346, C.347, L.373, Y.377, L.386, E.389, V.393, T.439, R.443, L.444, M.454 Ligand excluded by PLIP POV.18: 8 residues within 4Å: Chain B: C.342, M.345, C.346, Y.349, K.381, I.384, R.385, G.388 Ligand excluded by PLIP POV.23: 6 residues within 4Å: Chain C: M.435, M.442, G.449, V.452, P.453 Chain D: F.553 Ligand excluded by PLIP POV.24: 18 residues within 4Å: Chain B: I.341, M.345, I.348, Y.349, W.462, V.465 Chain C: C.494, W.495, A.498, V.499, L.502, Y.509, D.525, Y.526, P.527, L.530 Ligands: ECL.11, Y01.22 Ligand excluded by PLIP POV.25: 11 residues within 4Å: Chain C: C.346, C.347, L.373, Y.377, L.386, E.389, V.393, T.439, R.443, L.444, M.454 Ligand excluded by PLIP POV.26: 8 residues within 4Å: Chain C: C.342, M.345, C.346, Y.349, K.381, I.384, R.385, G.388 Ligand excluded by PLIP POV.27: 8 residues within 4Å: Chain D: C.342, M.345, C.346, Y.349, K.381, I.384, R.385, G.388 Ligand excluded by PLIP POV.32: 6 residues within 4Å: Chain A: F.553 Chain D: M.435, M.442, G.449, V.452, P.453 Ligand excluded by PLIP POV.33: 18 residues within 4Å: Chain C: I.341, M.345, I.348, Y.349, W.462, V.465 Chain D: C.494, W.495, A.498, V.499, L.502, Y.509, D.525, Y.526, P.527, L.530 Ligands: ECL.19, Y01.31 Ligand excluded by PLIP POV.34: 11 residues within 4Å: Chain D: C.346, C.347, L.373, Y.377, L.386, E.389, V.393, T.439, R.443, L.444, M.454 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: D.542 Chain B: D.542 Chain C: D.542 Chain D: D.542 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain D Metal complexes: B:D.542, B:D.542, C:D.542, C:D.542, D:D.542

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neuberger, A. et al., Structural mechanisms of TRPV6 inhibition by ruthenium red and econazole. Nat Commun (2021)

Release Date

2021-11-17

Peptides

Transient receptor potential cation channel subfamily V member 6: 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 6

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