SMTL ID : 8uzj.1

Alpha7-nicotinic acetylcholine receptor bound to epibatidine and ivermectin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 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.1: 5 residues within 4Å: Chain A: N.110, S.111, S.112, H.114 Chain E: K.191 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: K.191 Chain B: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain B: K.191 Chain C: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 5 residues within 4Å: Chain C: K.191 Chain D: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain D: K.191 Chain E: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 3 residues within 4Å: Chain A: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain E: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP)

5 x CA: CALCIUM ION(Non-covalent)

CA.11: 5 residues within 4Å: Chain A: V.42, E.44, E.172, W.173, R.205 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:V.42, A:E.44, A:E.172 CA.19: 5 residues within 4Å: Chain B: V.42, E.44, E.172, W.173, R.205 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.42, B:E.44, B:E.172 CA.25: 5 residues within 4Å: Chain C: V.42, E.44, E.172, W.173, R.205 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:V.42, C:E.44, C:E.172 CA.31: 5 residues within 4Å: Chain D: V.42, E.44, E.172, W.173, R.205 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:V.42, D:E.44, D:E.172 CA.37: 5 residues within 4Å: Chain E: V.42, E.44, E.172, W.173, R.205 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:V.42, E:E.44, E:E.172

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

NAG.12: 3 residues within 4Å: Chain A: N.67, S.69, E.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.67, A:S.69 NAG.20: 3 residues within 4Å: Chain B: N.67, S.69, E.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.67, B:S.69 NAG.26: 3 residues within 4Å: Chain C: N.67, S.69, E.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.67, C:S.69 NAG.32: 3 residues within 4Å: Chain D: N.67, S.69, E.70 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.67, D:S.69 NAG.38: 3 residues within 4Å: Chain E: N.67, S.69, E.70 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.67, E:S.69

5 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.13: 9 residues within 4Å: Chain A: W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.315, A:F.319, A:F.319, A:A.522 Hydrogen bonds: A:W.315 9Z9.21: 9 residues within 4Å: Chain B: W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.315, B:F.319, B:F.319, B:A.522 Hydrogen bonds: B:W.315 9Z9.27: 9 residues within 4Å: Chain C: W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.315, C:F.319, C:F.319, C:A.522 Hydrogen bonds: C:W.315 9Z9.33: 9 residues within 4Å: Chain D: W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.315, D:F.319, D:F.319, D:A.522 Hydrogen bonds: D:W.315 9Z9.39: 9 residues within 4Å: Chain E: W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.315, E:F.319, E:F.319, E:A.522 Hydrogen bonds: E:W.315

5 x EPJ: EPIBATIDINE(Non-covalent)

EPJ.14: 15 residues within 4Å: Chain A: Y.92, S.147, W.148, S.149, Y.187, C.189, C.190, Y.194 Chain B: W.54, N.106, V.107, L.108, Q.116, Y.117, L.118 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.92, A:W.148, A:Y.187, A:Y.194, B:W.54, B:L.118 Hydrogen bonds: A:Y.92, A:W.148 Water bridges: B:L.118 EPJ.22: 15 residues within 4Å: Chain B: Y.92, S.147, W.148, S.149, Y.187, C.189, C.190, Y.194 Chain C: W.54, N.106, V.107, L.108, Q.116, Y.117, L.118 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:Y.92, B:W.148, B:Y.187, B:Y.194, C:W.54, C:L.118 Hydrogen bonds: B:Y.92, B:W.148 Water bridges: C:L.118 EPJ.28: 15 residues within 4Å: Chain C: Y.92, S.147, W.148, S.149, Y.187, C.189, C.190, Y.194 Chain D: W.54, N.106, V.107, L.108, Q.116, Y.117, L.118 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.92, C:W.148, C:Y.187, C:Y.194, D:W.54, D:L.118 Hydrogen bonds: C:Y.92, C:W.148 Water bridges: D:L.118 EPJ.34: 15 residues within 4Å: Chain D: Y.92, S.147, W.148, S.149, Y.187, C.189, C.190, Y.194 Chain E: W.54, N.106, V.107, L.108, Q.116, Y.117, L.118 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:W.54, E:L.118, D:Y.92, D:W.148, D:Y.187, D:Y.194 Water bridges: E:L.118 Hydrogen bonds: D:Y.92, D:W.148 EPJ.40: 15 residues within 4Å: Chain A: W.54, N.106, V.107, L.108, Q.116, Y.117, L.118 Chain E: Y.92, S.147, W.148, S.149, Y.187, C.189, C.190, Y.194 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:Y.92, E:W.148, E:Y.187, E:Y.194, A:W.54, A:L.118 Hydrogen bonds: E:Y.92, E:W.148 Water bridges: A:L.118

5 x IVM: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside(Non-covalent)

IVM.15: 23 residues within 4Å: Chain A: L.208, L.212, N.213, I.216, P.217, V.219, L.220, A.223, F.252, D.548, F.549 Chain E: T.250, M.253, S.266, V.267, A.271, F.274, A.275, M.278, I.279, G.282, L.283 Ligands: POV.16 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:L.208, A:L.212, A:I.216, A:V.219, E:I.279, E:L.283 Hydrogen bonds: A:N.213 IVM.17: 23 residues within 4Å: Chain A: T.250, M.253, S.266, V.267, A.271, F.274, A.275, M.278, I.279, G.282, L.283 Chain B: L.208, L.212, N.213, I.216, P.217, V.219, L.220, A.223, F.252, D.548, F.549 Ligands: POV.18 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.208, B:L.212, B:I.216, B:V.219, A:I.279, A:L.283 IVM.23: 23 residues within 4Å: Chain B: T.250, M.253, S.266, V.267, A.271, F.274, A.275, M.278, I.279, G.282, L.283 Chain C: L.208, L.212, N.213, I.216, P.217, V.219, L.220, A.223, F.252, D.548, F.549 Ligands: POV.24 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.208, C:L.212, C:I.216, C:V.219, B:I.279, B:L.283 Hydrogen bonds: C:N.213 IVM.29: 23 residues within 4Å: Chain C: T.250, M.253, S.266, V.267, A.271, F.274, A.275, M.278, I.279, G.282, L.283 Chain D: L.208, L.212, N.213, I.216, P.217, V.219, L.220, A.223, F.252, D.548, F.549 Ligands: POV.30 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:I.279, C:L.283, D:L.208, D:L.212, D:I.216, D:V.219 Hydrogen bonds: D:N.213 IVM.35: 23 residues within 4Å: Chain D: T.250, M.253, S.266, V.267, A.271, F.274, A.275, M.278, I.279, G.282, L.283 Chain E: L.208, L.212, N.213, I.216, P.217, V.219, L.220, A.223, F.252, D.548, F.549 Ligands: POV.36 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:L.208, E:L.212, E:I.216, E:V.219, D:I.279, D:L.283

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

POV.16: 20 residues within 4Å: Chain A: L.220, A.223, L.224, L.226, L.227, L.230, R.321, M.322, K.323, R.517, L.520, M.521, S.524 Chain E: G.282, L.283, V.286, I.290, Q.293, G.302 Ligands: IVM.15 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:L.220, A:A.223, A:L.226, A:L.227, E:L.283, E:V.286 Salt bridges: A:R.517, A:R.517, A:R.517 Hydrogen bonds: E:Q.293 POV.18: 20 residues within 4Å: Chain A: G.282, L.283, V.286, I.290, Q.293, G.302 Chain B: L.220, A.223, L.224, L.226, L.227, L.230, R.321, M.322, K.323, R.517, L.520, M.521, S.524 Ligands: IVM.17 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.220, B:A.223, B:L.226, A:L.283, A:V.286 Salt bridges: B:R.517, B:R.517, B:R.517 Hydrogen bonds: A:Q.293 POV.24: 19 residues within 4Å: Chain B: G.282, L.283, V.286, I.290, Q.293, G.302 Chain C: L.220, A.223, L.224, L.226, L.227, L.230, R.321, M.322, R.517, L.520, M.521, S.524 Ligands: IVM.23 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.220, C:A.223, C:L.226, C:L.227, B:L.283, B:V.286 Salt bridges: C:R.517, C:R.517, C:R.517 Hydrogen bonds: B:Q.293 POV.30: 19 residues within 4Å: Chain C: G.282, L.283, V.286, I.290, Q.293, G.302 Chain D: L.220, A.223, L.224, L.226, L.227, L.230, R.321, M.322, R.517, L.520, M.521, S.524 Ligands: IVM.29 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.220, D:A.223, D:L.226, C:L.283, C:V.286 Salt bridges: D:R.517, D:R.517, D:R.517 Hydrogen bonds: C:Q.293 POV.36: 20 residues within 4Å: Chain D: G.282, L.283, V.286, I.290, Q.293, G.302 Chain E: L.220, A.223, L.224, L.226, L.227, L.230, R.321, M.322, K.323, R.517, L.520, M.521, S.524 Ligands: IVM.35 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:L.283, D:V.286, E:L.220, E:A.223, E:L.226 Hydrogen bonds: D:Q.293 Salt bridges: E:R.517, E:R.517, E:R.517

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burke, S.M. et al., Structural mechanisms of alpha 7 nicotinic receptor allosteric modulation and activation. Cell (2024)

Release Date

2024-02-21

Peptides

Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562

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