SMTL ID : 7k4b.1

Cryo-EM structure of human TRPV6 in complex with (4- phenylcyclohexyl)piperazine inhibitor cis-22a

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

5 x VUG: 1-[cis-4-(3-methylphenyl)cyclohexyl]-4-(pyridin-3-yl)piperazine(Non-covalent)

VUG.1: 13 residues within 4Å: Chain A: P.424, F.425, F.456, V.459, M.466, T.479, I.482, I.486 Chain B: F.504, M.554, I.557, T.558, A.561 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.424, A:F.425, A:V.459, A:T.479, A:I.482, A:I.486 VUG.13: 12 residues within 4Å: Chain A: M.554, I.557, T.558, A.561 Chain D: P.424, F.425, F.456, V.459, M.466, T.479, I.482, I.486 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:P.424, D:F.425, D:F.456, D:V.459, D:T.479, D:I.482, D:I.486 VUG.21: 14 residues within 4Å: Chain B: P.424, F.425, F.456, V.459, M.466, T.479, I.482, I.486 Chain C: F.504, M.554, I.557, T.558, A.561, I.565 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.424, B:F.425, B:V.459, B:T.479, B:I.482, B:I.486 VUG.34: 8 residues within 4Å: Chain A: G.579 Chain B: G.579, W.583 Chain C: I.575, G.579, W.583 Chain D: G.579, W.583 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:W.583, B:W.583 VUG.37: 11 residues within 4Å: Chain C: P.424, F.425, F.456, V.459, M.466, T.479, I.482, I.486 Chain D: M.554, I.557, T.558 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:P.424, C:F.425, C:V.459, C:T.479, C:I.482, C:I.486

8 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, P.424, F.425, H.426, I.429, Y.467, R.470 Ligands: PCW.12 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.332, A:I.335, A:Y.336, A:Y.339, 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:P.424, A:F.425 Salt bridges: A:H.426, A:H.426, A:R.470 Y01.14: 13 residues within 4Å: Chain A: L.551, F.553, S.556, I.557, I.564 Chain D: C.494, M.497, I.501, P.527, L.530, F.531, F.534 Ligands: PCW.56 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.553, A:I.557, A:I.564, D:I.501, D:L.530, D:F.534 Hydrogen bonds: A:S.556 Y01.18: 14 residues within 4Å: Chain A: C.494, M.497, I.501, P.527, L.530, F.531, F.534 Chain B: L.551, F.553, S.556, I.557, I.564 Ligands: PCW.3, PCW.19 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.501, A:L.530, A:F.534, B:F.553, B:I.557, B:I.564 Hydrogen bonds: B:S.556 Y01.22: 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, P.424, F.425, H.426, I.429, Y.467, R.470 Ligands: PCW.33 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.332, B:I.335, B:Y.336, B:Y.339, 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:P.424, B:F.425 Salt bridges: B:H.426, B:H.426, B:R.470 Y01.23: 13 residues within 4Å: Chain B: C.494, M.497, I.501, P.527, L.530, F.531, F.534 Chain C: L.551, F.553, S.556, I.557, I.564 Ligands: PCW.24 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.553, C:I.557, C:I.564, B:I.501, B:L.530, B:F.534 Hydrogen bonds: C:S.556 Y01.38: 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, P.424, F.425, H.426, I.429, Y.467, R.470 Ligands: PCW.48 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.332, C:I.335, C:Y.336, C:Y.339, 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:P.424, C:F.425 Salt bridges: C:H.426, C:H.426, C:R.470 Y01.52: 14 residues within 4Å: Chain C: C.494, M.497, I.501, P.527, L.530, F.531, F.534 Chain D: L.551, P.552, F.553, S.556, I.557, I.564 Ligands: PCW.39 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.553, D:I.557, D:I.564, C:I.501, C:L.530, C:F.534 Hydrogen bonds: D:F.553, D:S.556 Y01.55: 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, P.424, F.425, H.426, I.429, Y.467, R.470 Ligands: PCW.51 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.332, D:I.335, D:Y.336, D:Y.339, 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:P.424, D:F.425 Salt bridges: D:H.426, D:H.426, D:R.470

48 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)

PCW.3: 19 residues within 4Å: Chain A: C.494, W.495, A.498, V.499, L.502, Y.509, Q.513, D.525, Y.526, P.527 Chain D: L.337, T.344, M.345, I.348, Y.349 Ligands: PCW.7, Y01.18, PCW.19, PCW.51 Ligand excluded by PLIP PCW.4: 7 residues within 4Å: Chain A: V.427, L.428, T.431, M.435, F.456, F.487 Ligands: PCW.20 Ligand excluded by PLIP PCW.5: 4 residues within 4Å: Chain A: M.435, M.442, G.449 Ligands: PCW.20 Ligand excluded by PLIP PCW.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.7: 1 residues within 4Å: Ligands: PCW.3 Ligand excluded by PLIP PCW.8: 6 residues within 4Å: Chain A: M.331, L.332, M.603, K.607, C.611, L.612 Ligand excluded by PLIP PCW.9: 10 residues within 4Å: Chain A: F.343, C.346, C.347, Y.377, E.389, T.392, V.393, T.439, R.443, L.444 Ligand excluded by PLIP PCW.10: 4 residues within 4Å: Chain A: F.472, M.474, L.475 Chain B: W.495 Ligand excluded by PLIP PCW.11: 13 residues within 4Å: Chain A: K.322, R.326, C.330, M.331, G.333, A.334, L.337, V.465, A.469, F.472, L.475 Chain B: Q.24, W.495 Ligand excluded by PLIP PCW.12: 10 residues within 4Å: Chain A: I.335, L.338, I.341, C.342, M.345, Y.349, K.381, G.388 Ligands: Y01.2, PCW.24 Ligand excluded by PLIP PCW.15: 3 residues within 4Å: Chain A: F.553 Ligands: PCW.16, PCW.56 Ligand excluded by PLIP PCW.16: 7 residues within 4Å: Chain A: F.553, I.557 Chain D: V.452, F.456 Ligands: PCW.15, PCW.57, PCW.58 Ligand excluded by PLIP PCW.19: 4 residues within 4Å: Chain B: F.553 Ligands: PCW.3, Y01.18, PCW.20 Ligand excluded by PLIP PCW.20: 7 residues within 4Å: Chain A: V.452, F.456 Chain B: F.553, I.557 Ligands: PCW.4, PCW.5, PCW.19 Ligand excluded by PLIP PCW.24: 18 residues within 4Å: Chain A: T.344, M.345, I.348, Y.349 Chain B: C.494, W.495, A.498, V.499, L.502, Y.509, Q.513, D.525, Y.526, P.527 Ligands: PCW.12, Y01.23, PCW.28, PCW.35 Ligand excluded by PLIP PCW.25: 7 residues within 4Å: Chain B: V.427, L.428, T.431, M.435, F.456, F.487 Ligands: PCW.36 Ligand excluded by PLIP PCW.26: 4 residues within 4Å: Chain B: M.435, M.442, G.449 Ligands: PCW.36 Ligand excluded by PLIP PCW.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.28: 1 residues within 4Å: Ligands: PCW.24 Ligand excluded by PLIP PCW.29: 6 residues within 4Å: Chain B: M.331, L.332, M.603, K.607, C.611, L.612 Ligand excluded by PLIP PCW.30: 11 residues within 4Å: Chain B: F.343, C.346, C.347, Y.377, L.386, E.389, T.392, V.393, T.439, R.443, L.444 Ligand excluded by PLIP PCW.31: 4 residues within 4Å: Chain B: F.472, M.474, L.475 Chain C: W.495 Ligand excluded by PLIP PCW.32: 12 residues within 4Å: Chain B: R.326, C.330, M.331, G.333, A.334, L.337, V.465, A.469, F.472, L.475 Chain C: Q.24, W.495 Ligand excluded by PLIP PCW.33: 10 residues within 4Å: Chain B: I.335, L.338, I.341, C.342, M.345, Y.349, K.381, G.388 Ligands: Y01.22, PCW.39 Ligand excluded by PLIP PCW.35: 3 residues within 4Å: Chain C: F.553 Ligands: PCW.24, PCW.36 Ligand excluded by PLIP PCW.36: 7 residues within 4Å: Chain B: V.452, F.456 Chain C: F.553, I.557 Ligands: PCW.25, PCW.26, PCW.35 Ligand excluded by PLIP PCW.39: 18 residues within 4Å: Chain B: T.344, M.345, I.348, Y.349 Chain C: C.494, W.495, A.498, V.499, L.502, Y.509, Q.513, D.525, Y.526, P.527 Ligands: PCW.33, PCW.43, Y01.52, PCW.53 Ligand excluded by PLIP PCW.40: 7 residues within 4Å: Chain C: V.427, L.428, T.431, M.435, F.456, F.487 Ligands: PCW.54 Ligand excluded by PLIP PCW.41: 4 residues within 4Å: Chain C: M.435, M.442, G.449 Ligands: PCW.54 Ligand excluded by PLIP PCW.42: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.43: 1 residues within 4Å: Ligands: PCW.39 Ligand excluded by PLIP PCW.44: 6 residues within 4Å: Chain C: M.331, L.332, M.603, K.607, C.611, L.612 Ligand excluded by PLIP PCW.45: 10 residues within 4Å: Chain C: F.343, C.346, Y.377, L.386, E.389, T.392, V.393, T.439, R.443, L.444 Ligand excluded by PLIP PCW.46: 4 residues within 4Å: Chain C: F.472, M.474, L.475 Chain D: W.495 Ligand excluded by PLIP PCW.47: 13 residues within 4Å: Chain C: K.322, R.326, C.330, M.331, G.333, A.334, L.337, V.465, A.469, F.472, L.475 Chain D: Q.24, W.495 Ligand excluded by PLIP PCW.48: 10 residues within 4Å: Chain C: I.335, L.338, I.341, C.342, M.345, Y.349, K.381, G.388 Ligands: Y01.38, PCW.56 Ligand excluded by PLIP PCW.49: 4 residues within 4Å: Chain A: W.495 Chain D: F.472, M.474, L.475 Ligand excluded by PLIP PCW.50: 13 residues within 4Å: Chain A: Q.24, W.495 Chain D: K.322, R.326, C.330, M.331, G.333, A.334, L.337, V.465, A.469, F.472, L.475 Ligand excluded by PLIP PCW.51: 11 residues within 4Å: Chain D: I.335, L.338, I.341, C.342, M.345, Y.349, K.381, G.388, V.391 Ligands: PCW.3, Y01.55 Ligand excluded by PLIP PCW.53: 3 residues within 4Å: Chain D: F.553 Ligands: PCW.39, PCW.54 Ligand excluded by PLIP PCW.54: 7 residues within 4Å: Chain C: V.452, F.456 Chain D: F.553, I.557 Ligands: PCW.40, PCW.41, PCW.53 Ligand excluded by PLIP PCW.56: 18 residues within 4Å: Chain C: L.337, M.345, I.348, Y.349 Chain D: C.494, W.495, A.498, V.499, L.502, Y.509, Q.513, D.525, Y.526, P.527 Ligands: Y01.14, PCW.15, PCW.48, PCW.60 Ligand excluded by PLIP PCW.57: 6 residues within 4Å: Chain D: V.427, T.431, M.435, F.456, F.487 Ligands: PCW.16 Ligand excluded by PLIP PCW.58: 4 residues within 4Å: Chain D: M.435, M.442, G.449 Ligands: PCW.16 Ligand excluded by PLIP PCW.59: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.60: 1 residues within 4Å: Ligands: PCW.56 Ligand excluded by PLIP PCW.61: 6 residues within 4Å: Chain D: M.331, L.332, M.603, K.607, C.611, L.612 Ligand excluded by PLIP PCW.62: 10 residues within 4Å: Chain D: F.343, C.346, Y.377, E.389, T.392, V.393, T.439, M.440, R.443, L.444 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.17: 4 residues within 4Å: Chain A: D.542 Chain B: D.542 Chain C: D.542 Chain D: D.542 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Metal complexes: A:D.542, D:D.542

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhardwaj, R. et al., Inactivation-mimicking block of the epithelial calcium channel TRPV6. Sci Adv (2020)

Release Date

2020-12-09

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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