SMTL ID : 6pv7.1

Human alpha3beta4 nicotinic acetylcholine receptor in complex with nicotine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-3-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.24, S.26 Chain B: E.77 Chain H: T.58 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: N.24, S.26 Chain F: N.57 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 8 residues within 4Å: Chain A: N.141, T.143, K.180, Y.184, H.186, T.201, S.203, Y.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.184, A:H.186 NAG-NAG-BMA-MAN-MAN.4: 4 residues within 4Å: Chain B: N.145, R.188, D.204, I.206 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.188 NAG-NAG-BMA-MAN-MAN.6: 4 residues within 4Å: Chain C: N.145, R.188, D.204, I.206 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.188 NAG-NAG-BMA-MAN-MAN.8: 8 residues within 4Å: Chain D: N.141, T.143, K.180, Y.184, K.185, H.186, S.203, Y.205 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.186, D:K.185 NAG-NAG-BMA-MAN-MAN.10: 2 residues within 4Å: Chain E: N.145, R.188 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.188

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 2 residues within 4Å: Chain B: R.115, N.117 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 2 residues within 4Å: Chain C: R.115, N.117 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 1 residues within 4Å: Chain E: N.117 No protein-ligand interaction detected (PLIP)

2 x NCT: (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE(Non-covalent)

NCT.11: 8 residues within 4Å: Chain A: Y.93, W.149, C.192, C.193, Y.197 Chain B: W.59, I.113, L.123 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.59, B:I.113, B:L.123 Water bridges: B:L.123 NCT.24: 9 residues within 4Å: Chain D: Y.93, W.149, Y.190, C.192, C.193, Y.197 Chain E: W.59, I.113, L.123 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:W.59, E:I.113, E:L.123 Water bridges: E:L.123

10 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.12: 5 residues within 4Å: Chain A: V.289, I.290, F.293, F.499 Ligands: Y01.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.289, A:I.290, A:F.293, A:F.293, A:F.499 Y01.13: 4 residues within 4Å: Chain A: F.226, Y.233, L.500 Chain E: V.290 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:V.290, A:F.226, A:Y.233, A:Y.233, A:L.500, A:L.500 Y01.17: 7 residues within 4Å: Chain A: V.289 Chain B: L.227, I.230, Y.234, R.490, W.494 Ligands: Y01.12 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.289, B:L.227, B:I.230, B:Y.234, B:W.494 Hydrogen bonds: B:R.490 Y01.18: 3 residues within 4Å: Chain B: C.294, F.316, F.492 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.316, B:F.492 Y01.21: 7 residues within 4Å: Chain B: V.290 Chain C: L.227, I.230, Y.234, R.490, L.493, W.494 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.227, C:I.230, C:Y.234, C:L.493, C:W.494, B:V.290 Y01.22: 8 residues within 4Å: Chain C: F.287, V.290, T.291, C.294, F.316, V.488, F.492 Ligands: Y01.25 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.287, C:V.290, C:F.316, C:V.488 Y01.25: 5 residues within 4Å: Chain C: V.290, C.294 Chain D: Y.233, I.508 Ligands: Y01.22 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.508, C:V.290 Y01.26: 8 residues within 4Å: Chain D: T.285, L.286, V.289, I.290, F.293, F.315, F.499 Ligands: Y01.29 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:T.285, D:L.286, D:L.286, D:V.289, D:F.293, D:F.293, D:F.499 Y01.29: 7 residues within 4Å: Chain E: L.227, I.230, Y.234, R.490, L.493, W.494 Ligands: Y01.26 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:L.227, E:L.227, E:I.230, E:Y.234, E:L.493, E:W.494 Y01.30: 6 residues within 4Å: Chain E: F.287, V.290, C.294, V.312, F.316, F.492 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.290, E:F.492

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

NA.14: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.243

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.15: 1 residues within 4Å: Chain B: N.15 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain B: N.72, S.74 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.72 NAG.19: 3 residues within 4Å: Chain C: D.11, N.15, T.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.15 NAG.20: 3 residues within 4Å: Chain C: N.72, S.74, R.75 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.72, C:S.74, C:S.74, C:R.75 NAG.27: 2 residues within 4Å: Chain E: N.15, T.17 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.17, E:T.17 NAG.28: 3 residues within 4Å: Chain E: N.72, S.74, R.75 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.72, E:R.75

1 x DD9: nonane(Non-functional Binders)

DD9.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gharpure, A. et al., Agonist Selectivity and Ion Permeation in the alpha 3 beta 4 Ganglionic Nicotinic Receptor. Neuron (2019)

Release Date

2019-09-11

Peptides

Fusion protein of Neuronal acetylcholine receptor subunit alpha-3 and Soluble cytochrome b562: AD
Fusion protein of Neuronal acetylcholine receptor subunit beta-4 and Soluble cytochrome b562: BCE
IgG2b Fab heavy chain: FH
Kappa Fab light chain: GI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

E
E

F
F

H
H

G
G

I
I

Membrane

We predict this structure to be a membrane protein.
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Fusion protein of Neuronal acetylcholine receptor subunit alpha-3 and Soluble cytochrome b562

Fusion protein of Neuronal acetylcholine receptor subunit beta-4 and Soluble cytochrome b562

IgG2b Fab heavy chain

Kappa Fab light chain

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