SMTL ID : 8v8a.1

Alpha7-nicotinic acetylcholine receptor time resolved bound to epibatidine and PNU-120596 desensitized intermediate state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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.1: 3 residues within 4Å: Chain A: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain E: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP)

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.2: 4 residues within 4Å: Chain A: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 4 residues within 4Å: Chain B: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain C: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain D: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain E: N.110, S.111, S.112, H.114 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 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.42, A:E.44 CA.21: 5 residues within 4Å: Chain B: V.42, E.44, E.172, W.173, R.205 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:V.42, B:E.44 CA.29: 5 residues within 4Å: Chain C: V.42, E.44, E.172, W.173, R.205 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:V.42, C:E.44 CA.37: 5 residues within 4Å: Chain D: V.42, E.44, E.172, W.173, R.205 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:V.42, D:E.44 CA.45: 5 residues within 4Å: Chain E: V.42, E.44, E.172, W.173, R.205 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:V.42, E:E.44

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.22: 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.30: 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.38: 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.46: 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

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

POV.13: 22 residues within 4Å: Chain A: D.130, R.132, M.253, D.265, S.266, V.267, Q.272, A.275, M.278, I.279 Chain B: L.208, L.212, I.216, P.217, V.219, L.220, I.221, D.548, F.549 Ligands: POV.14, POV.19, I34.20 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.208, B:L.212, B:I.216, B:I.216, B:I.216, B:V.219, A:Q.272, A:M.278, A:I.279 Hydrogen bonds: A:R.132, A:V.267 POV.14: 15 residues within 4Å: Chain A: R.132, W.133, Q.272, A.275, S.276, I.279, I.280, F.526, C.530, G.533, I.534, S.537, P.539 Ligands: POV.13, I34.20 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.272, A:I.279, A:I.279, A:I.280, A:F.526, A:I.534 Hydrogen bonds: A:R.132 POV.17: 22 residues within 4Å: Chain A: L.220, I.221, A.223, L.224, L.226, L.227, L.230, R.321, M.322, R.517, L.520, M.521, S.524 Chain E: L.246, M.278, I.279, G.282, L.283, V.286, I.290, Q.293 Ligands: POV.47 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:L.224, A:L.224, A:L.226, A:L.230, E:L.283, E:V.286 Salt bridges: A:R.517 POV.19: 22 residues within 4Å: Chain A: L.246, M.278, I.279, G.282, L.283, V.286, I.290, Q.293 Chain B: L.220, I.221, A.223, L.224, L.226, L.227, L.230, R.321, M.322, R.517, L.520, M.521, S.524 Ligands: POV.13 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.283, A:V.286, B:L.224, B:L.224, B:L.226, B:L.230 Salt bridges: B:R.517 POV.23: 22 residues within 4Å: Chain B: D.130, R.132, M.253, D.265, S.266, V.267, Q.272, A.275, M.278, I.279 Chain C: L.208, L.212, I.216, P.217, V.219, L.220, I.221, D.548, F.549 Ligands: POV.24, POV.27, I34.28 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.208, C:L.212, C:I.216, C:I.216, C:I.216, C:V.219, B:Q.272, B:M.278, B:I.279 Hydrogen bonds: B:R.132, B:V.267 POV.24: 15 residues within 4Å: Chain B: R.132, W.133, Q.272, A.275, S.276, I.279, I.280, F.526, C.530, G.533, I.534, S.537, P.539 Ligands: POV.23, I34.28 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Q.272, B:I.279, B:I.279, B:I.280, B:F.526, B:I.534 Hydrogen bonds: B:R.132 POV.27: 22 residues within 4Å: Chain B: L.246, M.278, I.279, G.282, L.283, V.286, I.290, Q.293 Chain C: L.220, I.221, A.223, L.224, L.226, L.227, L.230, R.321, M.322, R.517, L.520, M.521, S.524 Ligands: POV.23 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.224, C:L.224, C:L.226, C:L.230, B:L.283, B:V.286 Salt bridges: C:R.517 POV.31: 22 residues within 4Å: Chain C: D.130, R.132, M.253, D.265, S.266, V.267, Q.272, A.275, M.278, I.279 Chain D: L.208, L.212, I.216, P.217, V.219, L.220, I.221, D.548, F.549 Ligands: POV.32, POV.35, I34.36 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:Q.272, C:M.278, C:I.279, D:L.208, D:L.212, D:I.216, D:I.216, D:I.216, D:V.219 Hydrogen bonds: C:R.132, C:V.267 POV.32: 15 residues within 4Å: Chain C: R.132, W.133, Q.272, A.275, S.276, I.279, I.280, F.526, C.530, G.533, I.534, S.537, P.539 Ligands: POV.31, I34.36 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Q.272, C:I.279, C:I.279, C:I.280, C:F.526, C:I.534 Hydrogen bonds: C:R.132 POV.35: 22 residues within 4Å: Chain C: L.246, M.278, I.279, G.282, L.283, V.286, I.290, Q.293 Chain D: L.220, I.221, A.223, L.224, L.226, L.227, L.230, R.321, M.322, R.517, L.520, M.521, S.524 Ligands: POV.31 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.224, D:L.224, D:L.226, D:L.230, C:L.283, C:V.286 Salt bridges: D:R.517 POV.39: 22 residues within 4Å: Chain D: D.130, R.132, M.253, D.265, S.266, V.267, Q.272, A.275, M.278, I.279 Chain E: L.208, L.212, I.216, P.217, V.219, L.220, I.221, D.548, F.549 Ligands: POV.40, POV.43, I34.44 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:Q.272, D:M.278, D:I.279, E:L.208, E:L.212, E:I.216, E:I.216, E:I.216, E:V.219 Hydrogen bonds: D:R.132, D:V.267 POV.40: 15 residues within 4Å: Chain D: R.132, W.133, Q.272, A.275, S.276, I.279, I.280, F.526, C.530, G.533, I.534, S.537, P.539 Ligands: POV.39, I34.44 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Q.272, D:I.279, D:I.279, D:I.280, D:F.526, D:I.534 Hydrogen bonds: D:R.132 POV.43: 22 residues within 4Å: Chain D: L.246, M.278, I.279, G.282, L.283, V.286, I.290, Q.293 Chain E: L.220, I.221, A.223, L.224, L.226, L.227, L.230, R.321, M.322, R.517, L.520, M.521, S.524 Ligands: POV.39 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:L.283, D:V.286, E:L.224, E:L.224, E:L.226, E:L.230 Salt bridges: E:R.517 POV.47: 22 residues within 4Å: Chain A: L.208, L.212, I.216, P.217, V.219, L.220, I.221, D.548, F.549 Chain E: D.130, R.132, M.253, D.265, S.266, V.267, Q.272, A.275, M.278, I.279 Ligands: POV.17, I34.18, POV.48 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:L.208, A:L.212, A:I.216, A:I.216, A:I.216, A:V.219, E:Q.272, E:M.278, E:I.279 Hydrogen bonds: E:R.132, E:V.267 POV.48: 15 residues within 4Å: Chain E: R.132, W.133, Q.272, A.275, S.276, I.279, I.280, F.526, C.530, G.533, I.534, S.537, P.539 Ligands: I34.18, POV.47 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:Q.272, E:I.279, E:I.279, E:I.280, E:F.526, E:I.534 Hydrogen bonds: E:R.132

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

9Z9.15: 11 residues within 4Å: Chain A: N.314, W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526, I.529 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.318, A:F.319, A:F.319, A:F.319, A:A.522, A:V.525 Hydrogen bonds: A:W.315 9Z9.25: 11 residues within 4Å: Chain B: N.314, W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526, I.529 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.318, B:F.319, B:F.319, B:F.319, B:A.522, B:V.525 Hydrogen bonds: B:W.315 9Z9.33: 11 residues within 4Å: Chain C: N.314, W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526, I.529 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.318, C:F.319, C:F.319, C:F.319, C:A.522, C:V.525 Hydrogen bonds: C:W.315 9Z9.41: 11 residues within 4Å: Chain D: N.314, W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526, I.529 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.318, D:F.319, D:F.319, D:F.319, D:A.522, D:V.525 Hydrogen bonds: D:W.315 9Z9.49: 11 residues within 4Å: Chain E: N.314, W.315, C.316, W.318, F.319, L.518, M.521, A.522, V.525, F.526, I.529 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:W.318, E:F.319, E:F.319, E:F.319, E:A.522, E:V.525 Hydrogen bonds: E:W.315

5 x EPJ: EPIBATIDINE(Non-covalent)

EPJ.16: 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 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.92, A:W.148, A:Y.187, A:Y.194, B:W.54, B:L.108, B:L.118 Hydrogen bonds: A:Y.92, A:W.148 Water bridges: B:L.118 Halogen bonds: B:Q.116 EPJ.26: 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 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:W.54, C:L.108, C:L.118, B:Y.92, B:W.148, B:Y.187, B:Y.194 Water bridges: C:L.118 Halogen bonds: C:Q.116 Hydrogen bonds: B:Y.92, B:W.148 EPJ.34: 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 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:W.54, D:L.108, D:L.118, 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.42: 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 11 PLIP interactions: 5 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:W.54, E:L.108, E:L.118, 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.50: 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 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:W.54, A:L.108, A:L.118, E:Y.92, E:W.148, E:Y.187, E:Y.194 Water bridges: A:L.118 Halogen bonds: A:Q.116 Hydrogen bonds: E:Y.92, E:W.148

5 x I34: N-(5-Chloro-2,4-dimethoxyphenyl)-N'-(5-methyl-3-isoxazolyl)-urea(Non-covalent)

I34.18: 19 residues within 4Å: Chain A: L.212, N.213, L.214, P.217, I.221, V.251, F.252, L.255 Chain E: T.250, M.253, L.254, A.257, V.267, A.271, Q.272, A.275, M.278 Ligands: POV.47, POV.48 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:P.217, E:V.267 Hydrogen bonds: A:N.213, A:N.213, A:N.213 I34.20: 19 residues within 4Å: Chain A: T.250, M.253, L.254, A.257, V.267, A.271, Q.272, A.275, M.278 Chain B: L.212, N.213, L.214, P.217, I.221, V.251, F.252, L.255 Ligands: POV.13, POV.14 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.267, B:P.217 Hydrogen bonds: B:N.213, B:N.213, B:N.213 I34.28: 19 residues within 4Å: Chain B: T.250, M.253, L.254, A.257, V.267, A.271, Q.272, A.275, M.278 Chain C: L.212, N.213, L.214, P.217, I.221, V.251, F.252, L.255 Ligands: POV.23, POV.24 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:V.267, C:P.217 Hydrogen bonds: C:N.213, C:N.213, C:N.213 I34.36: 19 residues within 4Å: Chain C: T.250, M.253, L.254, A.257, V.267, A.271, Q.272, A.275, M.278 Chain D: L.212, N.213, L.214, P.217, I.221, V.251, F.252, L.255 Ligands: POV.31, POV.32 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.217, C:V.267 Hydrogen bonds: D:N.213, D:N.213, D:N.213 I34.44: 19 residues within 4Å: Chain D: T.250, M.253, L.254, A.257, V.267, A.271, Q.272, A.275, M.278 Chain E: L.212, N.213, L.214, P.217, I.221, V.251, F.252, L.255 Ligands: POV.39, POV.40 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:P.217, D:V.267 Hydrogen bonds: E:N.213, E:N.213, E:N.213

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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