SMTL ID : 8yr2.1

Structure of NET-Nisoxetine in outward-open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x 41U: nisoxetine(Non-covalent)

41U.1: 15 residues within 4Å: Chain A: F.72, A.73, D.75, A.145, V.148, G.149, Y.151, Y.152, F.317, S.318, G.320, F.323, S.419, S.420, G.423 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.145, A:V.148, A:V.148, A:V.148, A:V.148, A:Y.152, A:F.323 Hydrogen bonds: A:F.72 41U.19: 15 residues within 4Å: Chain B: F.72, A.73, D.75, A.145, V.148, G.149, Y.151, Y.152, F.317, S.318, G.320, F.323, S.419, S.420, G.423 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.145, B:V.148, B:V.148, B:V.148, B:Y.152, B:F.323 Hydrogen bonds: B:F.72

2 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.2: 6 residues within 4Å: Chain A: Y.249, W.253, K.443, L.444, F.447 Ligands: CLR.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.444, A:F.447 Hydrogen bonds: A:Y.249, A:K.443 Salt bridges: A:K.443 PIO.20: 6 residues within 4Å: Chain B: Y.249, F.250, W.253, K.443, L.444, F.447 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.443, B:F.447 Hydrogen bonds: B:Y.249, B:K.443 Salt bridges: B:K.443

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: A.73, V.74, D.75, N.78, S.318, N.350 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.75, A:N.78, A:S.318, A:N.350 NA.4: 5 residues within 4Å: Chain A: G.71, V.74, L.415, D.418, S.419 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.415 NA.21: 6 residues within 4Å: Chain B: A.73, V.74, D.75, N.78, S.318, N.350 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.75, B:N.78, B:S.318, B:N.350 NA.22: 5 residues within 4Å: Chain B: G.71, V.74, L.415, D.418, S.419 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.419, B:S.419

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

CL.5: 7 residues within 4Å: Chain A: N.78, F.82, Y.98, Q.314, S.318, N.350, S.354 Ligand excluded by PLIP CL.23: 7 residues within 4Å: Chain B: N.78, F.82, Y.98, Q.314, S.318, N.350, S.354 Ligand excluded by PLIP

20 x CLR: CHOLESTEROL(Non-covalent)(Covalent)

CLR.6: 8 residues within 4Å: Chain A: L.438, H.441, L.444, G.448, F.451 Ligands: CLR.8, CLR.11, CLR.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.438, A:L.444, A:L.444, A:F.451 CLR.7: 4 residues within 4Å: Chain B: L.444 Ligands: CLR.8, 01.13, CLR.24 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.444 CLR.8: 11 residues within 4Å: Chain A: L.431, F.435, V.437, L.438, V.449, S.452 Ligands: CLR.6, CLR.7, 01.13, CLR.24, CLR.25 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.431, A:F.435, A:F.435, A:F.435, A:L.438, A:L.438, A:V.449 CLR.9: 12 residues within 4Å: Chain A: Y.147, I.227, H.228, I.230, L.456, F.459, V.468, L.472, W.553 Ligands: CLR.10, 01.13, CLR.26 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.147, A:I.230, A:F.459, A:V.468, A:V.468, A:L.472, A:W.553 CLR.10: 10 residues within 4Å: Chain A: Y.147, W.556, V.557, G.560, I.561, S.564 Ligands: CLR.9, 01.13, CLR.26, 01.30 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.556, A:V.557, A:V.557 CLR.11: 5 residues within 4Å: Chain A: L.444 Ligands: PIO.2, CLR.6, CLR.25, 01.29 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.444 CLR.12: 9 residues within 4Å: Chain A: P.233, W.235, L.238, F.451, L.455 Chain B: W.553 Ligands: 01.14, CLR.27, CLR.28 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.235, A:L.238, A:F.451, A:L.455, B:W.553 CLR.15: 6 residues within 4Å: Chain A: I.63, W.264, T.268, Y.271, F.272 Ligands: CLR.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.264, A:F.272, A:F.272 CLR.16: 6 residues within 4Å: Chain A: W.264, T.268, L.269, F.272, V.407 Ligands: CLR.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.264, A:W.264, A:T.268, A:L.269, A:F.272, A:V.407 CLR.17: 8 residues within 4Å: Chain A: T.99, L.102, I.103, M.107, Y.340, L.344, S.348, C.351 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.102, A:I.103, A:L.344 CLR.18: 9 residues within 4Å: Chain A: F.483, I.537, F.540, W.556, W.559, L.563, M.566, V.567, P.570 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.483, A:I.537, A:I.537, A:F.540, A:W.556, A:W.559, A:W.559, A:W.559, A:W.559, A:W.559, A:L.563, A:M.566, A:V.567, A:P.570 CLR.24: 9 residues within 4Å: Chain B: V.437, L.438, H.441, L.444, G.448, F.451 Ligands: CLR.7, CLR.8, CLR.25 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.438, B:L.444, B:F.451 CLR.25: 11 residues within 4Å: Chain B: L.431, F.435, V.437, L.438, V.449, S.452 Ligands: CLR.6, CLR.8, CLR.11, CLR.24, 01.29 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.431, B:F.435, B:F.435, B:F.435, B:V.437, B:L.438, B:L.438, B:V.449 CLR.26: 7 residues within 4Å: Chain A: W.553 Chain B: P.233, L.238, L.455 Ligands: CLR.9, CLR.10, 01.30 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.553, B:L.238, B:L.455 CLR.27: 10 residues within 4Å: Chain B: L.143, Y.147, I.227, I.230, L.456, V.468, L.472, W.553 Ligands: CLR.12, CLR.28 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.143, B:Y.147, B:I.230, B:L.472, B:W.553, B:W.553 CLR.28: 9 residues within 4Å: Chain B: Y.147, W.556, V.557, G.560, I.561, S.564 Ligands: CLR.12, 01.14, CLR.27 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.557, B:V.557, B:I.561 CLR.31: 9 residues within 4Å: Chain B: F.483, I.537, F.540, W.556, W.559, L.563, M.566, V.567, P.570 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.483, B:I.537, B:I.537, B:F.540, B:W.559, B:W.559, B:W.559, B:W.559, B:W.559, B:W.559, B:L.563, B:M.566, B:V.567, B:P.570 CLR.32: 6 residues within 4Å: Chain B: I.63, W.264, T.268, Y.271, F.272 Ligands: CLR.34 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.63, B:W.264, B:T.268, B:F.272 CLR.33: 8 residues within 4Å: Chain B: T.99, I.103, M.107, Y.340, L.344, S.348, C.351, I.352 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.103, B:I.103, B:L.344 Hydrogen bonds: B:Y.340 CLR.34: 6 residues within 4Å: Chain B: W.264, T.268, L.269, F.272, V.407 Ligands: CLR.32 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.264, B:T.268, B:L.269, B:F.272, B:F.272, B:F.272, B:V.407

4 x 01: [(2R)-2-octanoyloxy-3-[oxidanyl-[(2R,3R,5S,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

01.13: 12 residues within 4Å: Chain A: K.135, Y.139, D.434, F.435, S.564, L.568, Y.572, Y.575 Ligands: CLR.7, CLR.8, CLR.9, CLR.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.139, A:L.568 Hydrogen bonds: A:Y.139, A:Y.572 01.14: 6 residues within 4Å: Chain A: W.235, L.238, L.239, M.242 Ligands: CLR.12, CLR.28 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.238, A:L.239 01.29: 10 residues within 4Å: Chain B: Y.139, L.143, D.434, F.435, L.568, I.571, Y.572, Y.575 Ligands: CLR.11, CLR.25 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.139, B:Y.139, B:L.143, B:L.568, B:L.568, B:I.571 Hydrogen bonds: B:Y.139, B:D.434, B:D.434, B:Y.572, B:Y.575, B:Y.575 01.30: 6 residues within 4Å: Chain B: W.235, L.238, L.239, M.242 Ligands: CLR.10, CLR.26 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.238, B:L.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Dimerization and antidepressant recognition at noradrenaline transporter. Nature (2024)

Release Date

2024-05-29

Peptides

Sodium-dependent noradrenaline transporter: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Membrane

We predict this structure to be a membrane protein.
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Sodium-dependent noradrenaline transporter

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