SMTL ID : 7lgw.1

Structure of human Prestin in nanodisc in the presence of NaCl

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: F.101, F.137, S.396, L.397 Ligand excluded by PLIP CL.49: 4 residues within 4Å: Chain B: F.101, F.137, S.396, L.397 Ligand excluded by PLIP

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 9 residues within 4Å: Chain A: Y.486, T.490, I.493, I.494, L.497 Ligands: D10.7, D10.13, CLR.50, D10.61 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.486, A:Y.486, A:I.493, A:I.494, A:L.497 CLR.50: 11 residues within 4Å: Chain A: I.493 Chain B: I.240, Y.486, T.490, I.493, I.494, L.497 Ligands: CLR.2, D10.13, D10.55, D10.61 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.240, B:Y.486, B:I.493, B:I.494, B:L.497, A:I.493 Hydrogen bonds: B:Y.486, B:Y.486

38 x OCT: N-OCTANE(Non-functional Binders)(Non-covalent)

OCT.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.4: 8 residues within 4Å: Chain A: Y.204, V.492, L.496 Chain B: L.497, Y.501 Ligands: D10.12, D10.14, C14.78 Ligand excluded by PLIP OCT.5: 2 residues within 4Å: Ligands: OCT.6, D10.16 Ligand excluded by PLIP OCT.6: 4 residues within 4Å: Chain A: I.60, F.64, R.197 Ligands: OCT.5 Ligand excluded by PLIP OCT.8: 4 residues within 4Å: Chain A: F.241, Y.245, F.481 Ligands: OCT.9 Ligand excluded by PLIP OCT.9: 7 residues within 4Å: Chain A: F.241, T.474, V.477 Ligands: D10.7, OCT.8, OCT.27, C14.29 Ligand excluded by PLIP OCT.17: 1 residues within 4Å: Chain A: F.307 Ligand excluded by PLIP OCT.19: 8 residues within 4Å: Chain A: G.91, V.92, L.95, F.294, M.420, V.424, T.428 Ligands: D10.18 Ligand excluded by PLIP OCT.24: 1 residues within 4Å: Ligands: D12.23 Ligand excluded by PLIP OCT.27: 3 residues within 4Å: Ligands: OCT.9, D10.28, C14.30 Ligand excluded by PLIP OCT.37: 2 residues within 4Å: Chain A: M.267 Ligands: HP6.38 Ligand excluded by PLIP OCT.41: 4 residues within 4Å: Chain A: T.68, L.71, F.125 Ligands: OCT.42 Ligand excluded by PLIP OCT.42: 1 residues within 4Å: Ligands: OCT.41 Ligand excluded by PLIP OCT.43: 1 residues within 4Å: Chain A: Y.74 Ligand excluded by PLIP OCT.44: 2 residues within 4Å: Chain A: F.76, K.77 Ligand excluded by PLIP OCT.45: 2 residues within 4Å: Chain A: V.80, L.81 Ligand excluded by PLIP OCT.46: 1 residues within 4Å: Chain A: L.81 Ligand excluded by PLIP OCT.47: 6 residues within 4Å: Chain A: F.269, G.270, L.273, G.274, E.277 Ligands: OCT.48 Ligand excluded by PLIP OCT.48: 1 residues within 4Å: Ligands: OCT.47 Ligand excluded by PLIP OCT.51: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.52: 8 residues within 4Å: Chain A: L.497, Y.501 Chain B: Y.204, V.492, L.496 Ligands: C14.30, D10.60, D10.62 Ligand excluded by PLIP OCT.53: 2 residues within 4Å: Ligands: OCT.54, D10.64 Ligand excluded by PLIP OCT.54: 4 residues within 4Å: Chain B: I.60, F.64, R.197 Ligands: OCT.53 Ligand excluded by PLIP OCT.56: 5 residues within 4Å: Chain B: F.241, Y.245, F.481 Ligands: OCT.57, D10.87 Ligand excluded by PLIP OCT.57: 7 residues within 4Å: Chain B: F.241, T.474, V.477 Ligands: D10.55, OCT.56, OCT.75, C14.77 Ligand excluded by PLIP OCT.65: 1 residues within 4Å: Chain B: F.307 Ligand excluded by PLIP OCT.67: 8 residues within 4Å: Chain B: G.91, V.92, L.95, F.294, M.420, V.424, T.428 Ligands: D10.66 Ligand excluded by PLIP OCT.72: 1 residues within 4Å: Ligands: D12.71 Ligand excluded by PLIP OCT.75: 3 residues within 4Å: Ligands: OCT.57, D10.76, C14.78 Ligand excluded by PLIP OCT.84: 1 residues within 4Å: Chain B: G.263 Ligand excluded by PLIP OCT.88: 1 residues within 4Å: Chain B: Y.62 Ligand excluded by PLIP OCT.89: 4 residues within 4Å: Chain B: T.68, L.71, F.125 Ligands: OCT.90 Ligand excluded by PLIP OCT.90: 1 residues within 4Å: Ligands: OCT.89 Ligand excluded by PLIP OCT.91: 1 residues within 4Å: Chain B: Y.74 Ligand excluded by PLIP OCT.92: 2 residues within 4Å: Chain B: F.76, K.77 Ligand excluded by PLIP OCT.93: 2 residues within 4Å: Chain B: V.80, L.81 Ligand excluded by PLIP OCT.94: 1 residues within 4Å: Chain B: L.81 Ligand excluded by PLIP OCT.95: 5 residues within 4Å: Chain B: F.269, G.270, L.273, G.274, E.277 Ligand excluded by PLIP

33 x D10: DECANE(Non-functional Binders)(Non-covalent)

D10.7: 2 residues within 4Å: Ligands: CLR.2, OCT.9 Ligand excluded by PLIP D10.12: 6 residues within 4Å: Chain A: I.348, D.485, Y.486, L.488, I.489 Ligands: OCT.4 Ligand excluded by PLIP D10.13: 2 residues within 4Å: Ligands: CLR.2, CLR.50 Ligand excluded by PLIP D10.14: 4 residues within 4Å: Chain A: Y.204 Chain B: Q.504 Ligands: OCT.4, D10.76 Ligand excluded by PLIP D10.16: 3 residues within 4Å: Chain A: C.196 Ligands: OCT.5, D12.15 Ligand excluded by PLIP D10.18: 6 residues within 4Å: Chain A: V.298, T.301, G.302, L.431, F.432 Ligands: OCT.19 Ligand excluded by PLIP D10.20: 2 residues within 4Å: Chain A: L.423, L.426 Ligand excluded by PLIP D10.21: 1 residues within 4Å: Ligands: D10.22 Ligand excluded by PLIP D10.22: 5 residues within 4Å: Chain A: Y.118, L.326, P.327, F.388 Ligands: D10.21 Ligand excluded by PLIP D10.28: 4 residues within 4Å: Chain A: Y.501 Ligands: OCT.27, C14.30, D10.62 Ligand excluded by PLIP D10.31: 2 residues within 4Å: Chain A: L.458, W.462 Ligand excluded by PLIP D10.32: 4 residues within 4Å: Chain A: F.455, S.456, P.459 Ligands: D10.33 Ligand excluded by PLIP D10.33: 4 residues within 4Å: Chain A: M.453, F.455, S.456 Ligands: D10.32 Ligand excluded by PLIP D10.34: 6 residues within 4Å: Chain A: V.248, L.251, Q.252 Ligands: HP6.26, D10.35, D10.40 Ligand excluded by PLIP D10.35: 3 residues within 4Å: Chain A: L.251, V.254 Ligands: D10.34 Ligand excluded by PLIP D10.36: 2 residues within 4Å: Chain A: F.230, L.262 Ligand excluded by PLIP D10.40: 1 residues within 4Å: Ligands: D10.34 Ligand excluded by PLIP D10.55: 2 residues within 4Å: Ligands: CLR.50, OCT.57 Ligand excluded by PLIP D10.60: 6 residues within 4Å: Chain B: I.348, D.485, Y.486, L.488, I.489 Ligands: OCT.52 Ligand excluded by PLIP D10.61: 2 residues within 4Å: Ligands: CLR.2, CLR.50 Ligand excluded by PLIP D10.62: 4 residues within 4Å: Chain A: Q.504 Chain B: Y.204 Ligands: D10.28, OCT.52 Ligand excluded by PLIP D10.64: 3 residues within 4Å: Chain B: C.196 Ligands: OCT.53, D12.63 Ligand excluded by PLIP D10.66: 6 residues within 4Å: Chain B: V.298, T.301, G.302, L.431, F.432 Ligands: OCT.67 Ligand excluded by PLIP D10.68: 2 residues within 4Å: Chain B: L.423, L.426 Ligand excluded by PLIP D10.69: 1 residues within 4Å: Ligands: D10.70 Ligand excluded by PLIP D10.70: 5 residues within 4Å: Chain B: Y.118, L.326, P.327, F.388 Ligands: D10.69 Ligand excluded by PLIP D10.76: 4 residues within 4Å: Chain B: Y.501 Ligands: D10.14, OCT.75, C14.78 Ligand excluded by PLIP D10.79: 2 residues within 4Å: Chain B: L.458, W.462 Ligand excluded by PLIP D10.80: 4 residues within 4Å: Chain B: F.455, S.456, P.459 Ligands: D10.81 Ligand excluded by PLIP D10.81: 4 residues within 4Å: Chain B: M.453, F.455, S.456 Ligands: D10.80 Ligand excluded by PLIP D10.82: 6 residues within 4Å: Chain B: V.248, L.251, Q.252 Ligands: HP6.74, D10.83, D10.87 Ligand excluded by PLIP D10.83: 3 residues within 4Å: Chain B: L.251, V.254 Ligands: D10.82 Ligand excluded by PLIP D10.87: 2 residues within 4Å: Ligands: OCT.56, D10.82 Ligand excluded by PLIP

10 x D12: DODECANE(Non-covalent)

D12.10: 5 residues within 4Å: Chain A: C.192, T.333, F.336 Ligands: HEX.25, D12.39 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.333, A:F.336 D12.11: 3 residues within 4Å: Chain A: F.191, N.330, S.383 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.191 D12.15: 4 residues within 4Å: Chain A: C.196, R.197, F.200 Ligands: D10.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.200 D12.23: 3 residues within 4Å: Chain A: P.328, L.387 Ligands: OCT.24 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.328, A:L.387 D12.39: 4 residues within 4Å: Chain A: I.189, H.337, I.344 Ligands: D12.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.189, A:H.337, A:I.344 D12.58: 5 residues within 4Å: Chain B: C.192, T.333, F.336 Ligands: HEX.73, D12.86 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.333, B:F.336 D12.59: 3 residues within 4Å: Chain B: F.191, N.330, S.383 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.191 D12.63: 4 residues within 4Å: Chain B: C.196, R.197, F.200 Ligands: D10.64 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.200 D12.71: 3 residues within 4Å: Chain B: P.328, L.387 Ligands: OCT.72 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.328, B:L.387 D12.86: 4 residues within 4Å: Chain B: I.189, H.337, I.344 Ligands: D12.58 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.189, B:H.337, B:I.344

2 x HEX: HEXANE(Non-functional Binders)

HEX.25: 1 residues within 4Å: Ligands: D12.10 No protein-ligand interaction detected (PLIP) HEX.73: 1 residues within 4Å: Ligands: D12.58 No protein-ligand interaction detected (PLIP)

4 x HP6: HEPTANE(Non-covalent)

HP6.26: 4 residues within 4Å: Chain A: V.243, V.244, T.247 Ligands: D10.34 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.243, A:V.244 HP6.38: 5 residues within 4Å: Chain A: C.260, G.263, V.264, L.309 Ligands: OCT.37 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.264, A:L.309 HP6.74: 4 residues within 4Å: Chain B: V.243, V.244, T.247 Ligands: D10.82 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.243, B:V.244 HP6.85: 1 residues within 4Å: Chain B: M.267 No protein-ligand interaction detected (PLIP)

4 x C14: TETRADECANE(Non-covalent)

C14.29: 5 residues within 4Å: Chain A: K.466, T.470, L.473 Ligands: OCT.9, C14.30 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.466, A:T.470, A:L.473 C14.30: 7 residues within 4Å: Chain A: K.466, I.467, Y.501 Ligands: OCT.27, D10.28, C14.29, OCT.52 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.467 C14.77: 5 residues within 4Å: Chain B: K.466, T.470, L.473 Ligands: OCT.57, C14.78 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.466, B:T.470, B:L.473 C14.78: 7 residues within 4Å: Chain B: K.466, I.467, Y.501 Ligands: OCT.4, OCT.75, D10.76, C14.77 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.467

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ge, J. et al., Molecular mechanism of prestin electromotive signal amplification. Cell (2021)

Release Date

2021-08-25

Peptides

Prestin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Prestin

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