SMTL ID : 9cuj.1

Structure of human full-length derived TRPV6 channel in apo open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 20 residues within 4Å: Chain A: L.372, I.375, Y.376, Y.379, V.431, I.434, G.435, I.438, I.439, V.442, E.443, G.463, P.464, F.465, H.466, Y.507, R.510, M.643 Ligands: PCW.10, POV.13 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.372, A:Y.376, A:Y.379, A:Y.379, A:V.431, A:I.434, A:I.438, A:I.439, A:V.442, A:F.465, A:Y.507, A:Y.507 Hydrogen bonds: A:F.465 Salt bridges: A:H.466, A:H.466, A:R.510 Y01.2: 20 residues within 4Å: Chain A: P.464, F.465, L.468, S.495, F.496, V.499, C.503, M.506, R.510, T.519, I.520, Q.523, I.526, Q.636 Chain B: I.597, T.598, A.601, I.605 Ligands: POV.5, POV.19 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.464, A:L.468, A:F.496, A:V.499, A:Q.523, A:I.526, B:I.597, B:A.601, B:I.605 Hydrogen bonds: A:T.519, A:T.519, A:Q.636 Salt bridges: A:R.510 Y01.15: 14 residues within 4Å: Chain A: L.591, F.593, S.596, I.597, A.600, I.604, L.608 Chain D: C.534, M.537, P.567, L.570, F.574 Ligands: POV.16, POV.59 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.593, A:I.597, A:A.600, A:I.604, A:I.604, A:L.608, D:L.570, D:F.574, D:F.574 Y01.18: 14 residues within 4Å: Chain A: C.534, M.537, P.567, L.570, F.574 Chain B: L.591, F.593, S.596, I.597, A.600, I.604, L.608 Ligands: POV.4, POV.19 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.570, A:F.574, A:F.574, B:F.593, B:I.597, B:A.600, B:I.604, B:L.608 Y01.20: 19 residues within 4Å: Chain B: L.372, I.375, Y.376, Y.379, V.431, I.434, G.435, I.438, I.439, E.443, G.463, P.464, F.465, H.466, Y.507, R.510, M.643 Ligands: PCW.29, POV.32 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.372, B:Y.379, B:Y.379, B:V.431, B:I.434, B:I.438, B:I.439, B:F.465, B:Y.507, B:Y.507 Hydrogen bonds: B:F.465 Salt bridges: B:H.466, B:H.466, B:R.510 Y01.21: 19 residues within 4Å: Chain B: P.464, F.465, S.495, F.496, V.499, C.503, M.506, R.510, T.519, I.520, Q.523, I.526, Q.636 Chain C: I.597, T.598, A.601, I.605 Ligands: POV.24, POV.35 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:P.464, B:F.496, B:Q.523, B:I.526, C:I.597, C:A.601, C:I.605 Hydrogen bonds: B:T.519, B:T.519, B:Q.636 Salt bridges: B:R.510 Y01.34: 14 residues within 4Å: Chain B: C.534, M.537, P.567, L.570, F.574 Chain C: L.591, F.593, S.596, I.597, A.600, I.604, L.608 Ligands: POV.23, POV.35 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.570, B:F.574, B:F.574, C:F.593, C:I.597, C:A.600, C:I.604, C:L.608 Y01.36: 19 residues within 4Å: Chain C: L.372, I.375, Y.376, Y.379, V.431, I.434, G.435, I.438, I.439, E.443, G.463, P.464, F.465, H.466, Y.507, R.510, M.643 Ligands: PCW.45, POV.48 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.372, C:Y.379, C:Y.379, C:V.431, C:I.434, C:I.438, C:I.439, C:F.465, C:Y.507, C:Y.507 Hydrogen bonds: C:F.465 Salt bridges: C:H.466, C:H.466, C:R.510 Y01.37: 19 residues within 4Å: Chain C: P.464, F.465, S.495, F.496, V.499, C.503, M.506, R.510, T.519, I.520, Q.523, I.526, Q.636 Chain D: I.597, T.598, A.601, I.605 Ligands: POV.40, POV.55 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: D:I.597, D:A.601, C:P.464, C:F.496, C:Q.523, C:I.526 Hydrogen bonds: C:T.519, C:T.519, C:Q.636 Salt bridges: C:R.510 Y01.54: 14 residues within 4Å: Chain C: C.534, M.537, P.567, L.570, F.574 Chain D: L.591, F.593, S.596, I.597, A.600, I.604, L.608 Ligands: POV.39, POV.55 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.593, D:I.597, D:A.600, D:I.604, D:L.608, C:L.570, C:F.574, C:F.574 Y01.56: 19 residues within 4Å: Chain D: L.372, I.375, Y.376, Y.379, V.431, I.434, G.435, I.438, I.439, E.443, G.463, P.464, F.465, H.466, Y.507, R.510, M.643 Ligands: POV.52, PCW.65 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.372, D:Y.379, D:Y.379, D:V.431, D:I.434, D:I.438, D:I.439, D:F.465, D:Y.507, D:Y.507 Hydrogen bonds: D:F.465 Salt bridges: D:H.466, D:H.466, D:R.510 Y01.57: 19 residues within 4Å: Chain A: I.597, T.598, A.601, I.605 Chain D: P.464, F.465, S.495, F.496, V.499, C.503, M.506, R.510, T.519, I.520, Q.523, I.526, Q.636 Ligands: POV.16, POV.60 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:P.464, D:F.496, D:Q.523, D:I.526, A:I.597, A:A.601 Hydrogen bonds: D:T.519, D:Q.636 Salt bridges: D:R.510

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

POV.3: 8 residues within 4Å: Chain A: M.475, M.482, S.488, G.489, V.492 Ligands: POV.5, POV.7, POV.19 Ligand excluded by PLIP POV.4: 18 residues within 4Å: Chain A: W.535, A.538, Y.549, Q.553, D.565, Y.566, P.567, L.570 Chain D: I.381, M.385, I.388, Y.389 Ligands: PCW.8, Y01.18, POV.19, PCW.50, POV.51, POV.52 Ligand excluded by PLIP POV.5: 20 residues within 4Å: Chain A: I.460, L.461, P.464, V.467, L.468, T.471, F.496, L.500, Q.523, K.524, I.526, F.527, G.528, R.624 Chain B: A.601, I.604 Ligands: Y01.2, POV.3, PCW.9, POV.19 Ligand excluded by PLIP POV.6: 13 residues within 4Å: Chain A: F.383, C.386, C.387, Y.417, L.426, E.429, T.432, V.433, V.476, T.479, M.480, R.483, L.484 Ligand excluded by PLIP POV.7: 4 residues within 4Å: Chain A: F.474, V.481, A.487 Ligands: POV.3 Ligand excluded by PLIP POV.12: 20 residues within 4Å: Chain A: R.366, P.367, C.370, M.371, G.373, A.374, I.375, L.377, L.378, V.505, M.506, F.508, F.512, Q.513, L.515 Chain B: W.535, L.536, V.539 Ligands: PCW.11, POV.23 Ligand excluded by PLIP POV.13: 17 residues within 4Å: Chain A: I.375, L.378, Y.379, I.381, C.382, M.385, C.386, Y.389, K.421, I.424, R.425, V.427 Ligands: Y01.1, PCW.11, PCW.14, POV.23, PCW.27 Ligand excluded by PLIP POV.16: 12 residues within 4Å: Chain A: P.592, F.593, I.597, A.600, A.601 Chain D: F.496 Ligands: Y01.15, Y01.57, POV.58, POV.59, POV.60, PCW.63 Ligand excluded by PLIP POV.19: 11 residues within 4Å: Chain A: F.496 Chain B: P.592, F.593, I.597, A.601 Ligands: Y01.2, POV.3, POV.4, POV.5, PCW.8, Y01.18 Ligand excluded by PLIP POV.22: 9 residues within 4Å: Chain B: M.475, M.482, S.488, G.489, V.492, F.496 Ligands: POV.24, POV.26, POV.35 Ligand excluded by PLIP POV.23: 20 residues within 4Å: Chain A: L.377, I.381, M.385, I.388, Y.389 Chain B: W.535, A.538, L.542, Y.549, Q.553, D.565, Y.566, P.567, L.570 Ligands: PCW.11, POV.12, POV.13, PCW.27, Y01.34, POV.35 Ligand excluded by PLIP POV.24: 19 residues within 4Å: Chain B: I.460, L.461, P.464, L.468, T.471, F.496, L.500, Q.523, K.524, I.526, F.527, G.528, R.624 Chain C: A.601, I.604 Ligands: Y01.21, POV.22, PCW.28, POV.35 Ligand excluded by PLIP POV.25: 14 residues within 4Å: Chain B: F.383, C.386, C.387, Y.417, L.426, E.429, T.432, V.433, V.476, T.479, M.480, R.483, L.484, M.494 Ligand excluded by PLIP POV.26: 5 residues within 4Å: Chain B: F.474, V.478, V.481, A.487 Ligands: POV.22 Ligand excluded by PLIP POV.31: 20 residues within 4Å: Chain B: R.366, P.367, C.370, M.371, G.373, A.374, I.375, L.377, L.378, V.505, M.506, F.508, F.512, Q.513, L.515 Chain C: W.535, L.536, V.539 Ligands: PCW.30, POV.39 Ligand excluded by PLIP POV.32: 16 residues within 4Å: Chain B: I.375, L.378, Y.379, I.381, C.382, M.385, C.386, Y.389, K.421, R.425, V.427 Ligands: Y01.20, PCW.30, PCW.33, POV.39, PCW.43 Ligand excluded by PLIP POV.35: 11 residues within 4Å: Chain B: F.496 Chain C: P.592, F.593, A.600, A.601 Ligands: Y01.21, POV.22, POV.23, POV.24, PCW.27, Y01.34 Ligand excluded by PLIP POV.38: 8 residues within 4Å: Chain C: M.475, S.488, G.489, V.492, F.496 Ligands: POV.40, POV.42, POV.55 Ligand excluded by PLIP POV.39: 20 residues within 4Å: Chain B: I.381, M.385, I.388, Y.389 Chain C: C.534, W.535, A.538, L.542, Y.549, Q.553, D.565, Y.566, P.567, L.570 Ligands: PCW.30, POV.31, POV.32, PCW.43, Y01.54, POV.55 Ligand excluded by PLIP POV.40: 19 residues within 4Å: Chain C: I.460, L.461, P.464, L.468, T.471, F.496, L.500, Q.523, K.524, I.526, F.527, G.528, R.624 Chain D: A.601, I.604 Ligands: Y01.37, POV.38, PCW.44, POV.55 Ligand excluded by PLIP POV.41: 14 residues within 4Å: Chain C: F.383, C.386, C.387, Y.417, L.426, E.429, T.432, V.433, V.476, T.479, M.480, R.483, L.484, M.494 Ligand excluded by PLIP POV.42: 5 residues within 4Å: Chain C: F.474, V.478, V.481, A.487 Ligands: POV.38 Ligand excluded by PLIP POV.47: 19 residues within 4Å: Chain C: R.366, P.367, C.370, M.371, G.373, A.374, L.377, L.378, V.505, M.506, F.508, F.512, Q.513, L.515 Chain D: W.535, L.536, V.539 Ligands: PCW.46, POV.59 Ligand excluded by PLIP POV.48: 16 residues within 4Å: Chain C: I.375, L.378, Y.379, I.381, C.382, M.385, C.386, Y.389, K.421, R.425, V.427 Ligands: Y01.36, PCW.46, PCW.49, POV.59, PCW.63 Ligand excluded by PLIP POV.51: 19 residues within 4Å: Chain A: W.535, L.536, V.539 Chain D: R.366, P.367, C.370, M.371, G.373, A.374, L.377, L.378, V.505, M.506, F.508, F.512, Q.513, L.515 Ligands: POV.4, PCW.50 Ligand excluded by PLIP POV.52: 16 residues within 4Å: Chain D: I.375, L.378, Y.379, I.381, C.382, M.385, C.386, Y.389, K.421, R.425, V.427 Ligands: POV.4, PCW.8, PCW.50, PCW.53, Y01.56 Ligand excluded by PLIP POV.55: 11 residues within 4Å: Chain C: F.496 Chain D: P.592, F.593, A.600, A.601 Ligands: Y01.37, POV.38, POV.39, POV.40, PCW.43, Y01.54 Ligand excluded by PLIP POV.58: 9 residues within 4Å: Chain D: M.475, M.482, S.488, G.489, V.492, F.496 Ligands: POV.16, POV.60, POV.62 Ligand excluded by PLIP POV.59: 20 residues within 4Å: Chain C: I.381, M.385, I.388, Y.389 Chain D: C.534, W.535, A.538, L.542, Y.549, Q.553, D.565, Y.566, P.567, L.570 Ligands: Y01.15, POV.16, PCW.46, POV.47, POV.48, PCW.63 Ligand excluded by PLIP POV.60: 19 residues within 4Å: Chain A: A.601, I.604 Chain D: I.460, L.461, P.464, L.468, T.471, F.496, L.500, Q.523, K.524, I.526, F.527, G.528, R.624 Ligands: POV.16, Y01.57, POV.58, PCW.64 Ligand excluded by PLIP POV.61: 14 residues within 4Å: Chain D: F.383, C.386, C.387, Y.417, L.426, E.429, T.432, V.433, V.476, T.479, M.480, R.483, L.484, M.494 Ligand excluded by PLIP POV.62: 5 residues within 4Å: Chain D: F.474, V.478, V.481, A.487 Ligands: POV.58 Ligand excluded by PLIP

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

PCW.8: 3 residues within 4Å: Ligands: POV.4, POV.19, POV.52 Ligand excluded by PLIP PCW.9: 2 residues within 4Å: Ligands: POV.5, PCW.50 Ligand excluded by PLIP PCW.10: 4 residues within 4Å: Chain A: M.643, L.644, K.647 Ligands: Y01.1 Ligand excluded by PLIP PCW.11: 8 residues within 4Å: Chain A: F.512, M.514, L.515 Chain B: W.535 Ligands: POV.12, POV.13, POV.23, PCW.28 Ligand excluded by PLIP PCW.14: 5 residues within 4Å: Chain A: L.378, I.381, M.385, I.424 Ligands: POV.13 Ligand excluded by PLIP PCW.27: 3 residues within 4Å: Ligands: POV.13, POV.23, POV.35 Ligand excluded by PLIP PCW.28: 2 residues within 4Å: Ligands: PCW.11, POV.24 Ligand excluded by PLIP PCW.29: 4 residues within 4Å: Chain B: M.643, L.644, K.647 Ligands: Y01.20 Ligand excluded by PLIP PCW.30: 9 residues within 4Å: Chain B: F.512, M.514, L.515 Chain C: M.531, W.535 Ligands: POV.31, POV.32, POV.39, PCW.44 Ligand excluded by PLIP PCW.33: 5 residues within 4Å: Chain B: L.378, I.381, M.385, I.424 Ligands: POV.32 Ligand excluded by PLIP PCW.43: 3 residues within 4Å: Ligands: POV.32, POV.39, POV.55 Ligand excluded by PLIP PCW.44: 2 residues within 4Å: Ligands: PCW.30, POV.40 Ligand excluded by PLIP PCW.45: 4 residues within 4Å: Chain C: M.643, L.644, K.647 Ligands: Y01.36 Ligand excluded by PLIP PCW.46: 9 residues within 4Å: Chain C: F.512, M.514, L.515 Chain D: M.531, W.535 Ligands: POV.47, POV.48, POV.59, PCW.64 Ligand excluded by PLIP PCW.49: 5 residues within 4Å: Chain C: L.378, I.381, M.385, I.424 Ligands: POV.48 Ligand excluded by PLIP PCW.50: 8 residues within 4Å: Chain A: W.535 Chain D: F.512, M.514, L.515 Ligands: POV.4, PCW.9, POV.51, POV.52 Ligand excluded by PLIP PCW.53: 5 residues within 4Å: Chain D: L.378, I.381, M.385, I.424 Ligands: POV.52 Ligand excluded by PLIP PCW.63: 3 residues within 4Å: Ligands: POV.16, POV.48, POV.59 Ligand excluded by PLIP PCW.64: 2 residues within 4Å: Ligands: PCW.46, POV.60 Ligand excluded by PLIP PCW.65: 4 residues within 4Å: Chain D: M.643, L.644, K.647 Ligands: Y01.56 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.17: 4 residues within 4Å: Chain A: D.582 Chain B: D.582 Chain C: D.582 Chain D: D.582 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain D Metal complexes: C:D.582, A:D.582, B:D.582, B:D.582, D:D.582

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neuberger, A. et al., Structure-function analyses of human TRPV6 ancestral and derived haplotypes. Structure (2024)

Release Date

2024-11-13

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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