SMTL ID : 8v80.1

Alpha7-nicotinic acetylcholine receptor bound to epibatidine and (-)-TQS

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: 4 residues within 4Å: Chain A: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain B: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain C: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain D: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: 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:E.44, A:E.172, 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:E.44, B:E.172, B:E.172 CA.26: 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:E.44, C:E.172, C:E.172 CA.33: 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:E.44, D:E.172, D:E.172 CA.40: 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:E.44, E:E.172, 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.27: 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.34: 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.41: 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

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

POV.13: 18 residues within 4Å: Chain A: Y.128, D.130, R.132, W.133, D.265, S.266, V.267, Q.272, A.275, I.279, L.283 Chain B: L.208, L.212, I.216, L.220, F.549 Ligands: YLR.16, POV.18 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.267, A:Q.272, A:A.275, A:I.279, B:I.216, B:L.220, B:F.549, B:F.549 Hydrogen bonds: A:V.267 Salt bridges: A:D.130, A:R.132 POV.17: 20 residues within 4Å: Chain A: L.220, A.223, L.224, L.226, L.227, L.230, R.321, M.322, R.517, L.520, S.524 Chain E: I.279, G.282, L.283, V.286, I.290, Q.293, G.302 Ligands: POV.42, YLR.45 7 PLIP interactions: 2 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:V.286, A:A.223, A:L.224, A:L.230 Hydrogen bonds: E:Q.293, A:R.517 Salt bridges: A:R.517 POV.18: 20 residues within 4Å: Chain A: I.279, 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, R.517, L.520, S.524 Ligands: POV.13, YLR.16 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.286, B:A.223, B:L.224, B:L.230 Hydrogen bonds: A:Q.293, B:R.517 Salt bridges: B:R.517 POV.21: 18 residues within 4Å: Chain B: Y.128, D.130, R.132, W.133, D.265, S.266, V.267, Q.272, A.275, I.279, L.283 Chain C: L.208, L.212, I.216, L.220, F.549 Ligands: POV.22, YLR.25 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:V.267, B:Q.272, B:A.275, B:I.279, C:I.216, C:L.220, C:F.549, C:F.549 Hydrogen bonds: B:V.267 Salt bridges: B:D.130, B:R.132 POV.22: 20 residues within 4Å: Chain B: I.279, 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, S.524 Ligands: POV.21, YLR.25 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.223, C:L.224, C:L.230, B:V.286 Hydrogen bonds: C:R.517, B:Q.293 Salt bridges: C:R.517 POV.28: 18 residues within 4Å: Chain C: Y.128, D.130, R.132, W.133, D.265, S.266, V.267, Q.272, A.275, I.279, L.283 Chain D: L.208, L.212, I.216, L.220, F.549 Ligands: POV.29, YLR.32 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:L.208, D:I.216, D:L.220, D:F.549, D:F.549, C:V.267, C:Q.272, C:A.275, C:I.279 Hydrogen bonds: C:V.267 Salt bridges: C:D.130, C:R.132 POV.29: 20 residues within 4Å: Chain C: I.279, 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, S.524 Ligands: POV.28, YLR.32 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.223, D:L.224, D:L.230, C:V.286 Hydrogen bonds: D:R.517, C:Q.293 Salt bridges: D:R.517 POV.35: 18 residues within 4Å: Chain D: Y.128, D.130, R.132, W.133, D.265, S.266, V.267, Q.272, A.275, I.279, L.283 Chain E: L.208, L.212, I.216, L.220, F.549 Ligands: POV.36, YLR.39 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:V.267, D:Q.272, D:A.275, D:I.279, E:I.216, E:L.220, E:F.549, E:F.549 Hydrogen bonds: D:V.267 Salt bridges: D:D.130, D:R.132 POV.36: 20 residues within 4Å: Chain D: I.279, 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, R.517, L.520, S.524 Ligands: POV.35, YLR.39 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:A.223, E:L.224, E:L.230, D:V.286 Hydrogen bonds: E:R.517, D:Q.293 Salt bridges: E:R.517 POV.42: 18 residues within 4Å: Chain A: L.208, L.212, I.216, L.220, F.549 Chain E: Y.128, D.130, R.132, W.133, D.265, S.266, V.267, Q.272, A.275, I.279, L.283 Ligands: POV.17, YLR.45 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain E Hydrophobic interactions: A:L.208, A:I.216, A:L.220, A:F.549, A:F.549, E:V.267, E:Q.272, E:A.275, E:I.279 Hydrogen bonds: E:V.267 Salt bridges: E:D.130, E:R.132

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

9Z9.14: 9 residues within 4Å: Chain A: W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.315, A:W.318, A:F.319, A:F.319, A:V.525, A:V.525, A:F.526 Hydrogen bonds: A:W.315 9Z9.23: 9 residues within 4Å: Chain B: W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.315, B:W.318, B:F.319, B:F.319, B:V.525, B:V.525, B:F.526 Hydrogen bonds: B:W.315 9Z9.30: 9 residues within 4Å: Chain C: W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.315, C:W.318, C:F.319, C:F.319, C:V.525, C:V.525, C:F.526 Hydrogen bonds: C:W.315 9Z9.37: 9 residues within 4Å: Chain D: W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.315, D:W.318, D:F.319, D:F.319, D:V.525, D:V.525, D:F.526 Hydrogen bonds: D:W.315 9Z9.43: 9 residues within 4Å: Chain E: W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:W.315, E:W.318, E:F.319, E:F.319, E:V.525, E:V.525, E:F.526 Hydrogen bonds: E:W.315

5 x EPJ: EPIBATIDINE(Non-covalent)

EPJ.15: 14 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, 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 Hydrogen bonds: A:Y.92, A:W.148 Water bridges: B:L.118 Halogen bonds: B:Q.116 EPJ.24: 14 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, 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 Hydrogen bonds: B:Y.92, B:W.148 Water bridges: C:L.118 Halogen bonds: C:Q.116 EPJ.31: 14 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, L.108, Q.116, Y.117, L.118 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:W.54, C:Y.92, C:W.148, C:Y.187, C:Y.194 Water bridges: D:L.118 Halogen bonds: D:Q.116 Hydrogen bonds: C:Y.92, C:W.148 EPJ.38: 14 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, 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, D:Y.92, D:W.148, D:Y.187, D:Y.194 Water bridges: E:L.118 Halogen bonds: E:Q.116 Hydrogen bonds: D:Y.92, D:W.148 EPJ.44: 14 residues within 4Å: Chain A: W.54, N.106, 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 Hydrogen bonds: E:Y.92, E:W.148 Water bridges: A:L.118 Halogen bonds: A:Q.116

5 x YLR: (3aR,4S,9bS)-4-(naphthalen-1-yl)-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-8-sulfonamide(Non-covalent)

YLR.16: 20 residues within 4Å: Chain A: L.246, M.253, V.256, A.257, A.271, F.274, A.275, M.278, I.279, G.282 Chain B: L.212, N.213, I.216, P.217, L.220, I.221, L.224, F.252 Ligands: POV.13, POV.18 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.216, B:P.217, B:L.220, B:I.221, B:L.224, A:M.253, A:F.274, A:M.278 Hydrogen bonds: B:N.213, A:A.257 YLR.25: 20 residues within 4Å: Chain B: L.246, M.253, V.256, A.257, A.271, F.274, A.275, M.278, I.279, G.282 Chain C: L.212, N.213, I.216, P.217, L.220, I.221, L.224, F.252 Ligands: POV.21, POV.22 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:M.253, B:F.274, B:M.278, C:I.216, C:P.217, C:L.220, C:I.221, C:L.224 Hydrogen bonds: B:A.257, C:N.213 YLR.32: 20 residues within 4Å: Chain C: L.246, M.253, V.256, A.257, A.271, F.274, A.275, M.278, I.279, G.282 Chain D: L.212, N.213, I.216, P.217, L.220, I.221, L.224, F.252 Ligands: POV.28, POV.29 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.216, D:P.217, D:L.220, D:I.221, D:L.224, C:M.253, C:F.274, C:M.278 Hydrogen bonds: D:N.213, C:A.257 YLR.39: 20 residues within 4Å: Chain D: L.246, M.253, V.256, A.257, A.271, F.274, A.275, M.278, I.279, G.282 Chain E: L.212, N.213, I.216, P.217, L.220, I.221, L.224, F.252 Ligands: POV.35, POV.36 10 PLIP interactions: 6 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:I.216, E:P.217, E:L.220, E:I.221, E:L.224, D:M.253, D:F.274, D:M.278 Hydrogen bonds: E:N.213, D:A.257 YLR.45: 20 residues within 4Å: Chain A: L.212, N.213, I.216, P.217, L.220, I.221, L.224, F.252 Chain E: L.246, M.253, V.256, A.257, A.271, F.274, A.275, M.278, I.279, G.282 Ligands: POV.17, POV.42 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: A:I.216, A:P.217, A:L.220, A:I.221, A:L.224, E:M.253, E:F.274, E:M.278 Hydrogen bonds: A:N.213, E:A.257

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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