SMTL ID : 8ut1.1

Alpha7-nicotinic acetylcholine receptor bound to epibatidine

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 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.44 CA.19: 5 residues within 4Å: Chain B: V.42, E.44, E.172, W.173, R.205 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.44 CA.26: 5 residues within 4Å: Chain C: V.42, E.44, E.172, W.173, R.205 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.44 CA.33: 5 residues within 4Å: Chain D: V.42, E.44, E.172, W.173, R.205 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.44 CA.40: 5 residues within 4Å: Chain E: V.42, E.44, E.172, W.173, R.205 1 PLIP interactions: 1 interactions with chain E Metal complexes: 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:S.69, A:E.70 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:S.69, B:E.70 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:S.69, C:E.70 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:S.69, D:E.70 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:S.69, E:E.70

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

POV.13: 17 residues within 4Å: Chain A: Y.128, D.130, R.132, D.265, S.266, V.267, Q.272, A.275, I.279 Chain B: L.208, L.212, I.216, P.217, L.220, D.548, F.549 Ligands: POV.14 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.267, A:V.267, A:Q.272, A:I.279, B:L.208, B:I.216, B:I.216, B:F.549 Hydrogen bonds: A:V.267 Salt bridges: A:D.130, A:R.132 POV.14: 14 residues within 4Å: Chain A: R.132, W.133, Q.272, A.275, S.276, I.279, I.280, F.526, I.529, C.530, G.533, I.534, S.537 Ligands: POV.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.275, A:F.526 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, M.521, S.524 Chain E: I.279, G.282, L.283, V.286, I.290, Q.293, G.302, K.303 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:V.286, E:I.290, A:L.230 Hydrogen bonds: E:Q.293 Salt bridges: A:R.517, 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, K.303 Chain B: L.220, A.223, L.224, L.226, L.227, L.230, R.321, M.322, R.517, L.520, M.521, S.524 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.286, A:I.290, B:L.230 Hydrogen bonds: A:Q.293 Salt bridges: B:R.517, B:R.517 POV.21: 17 residues within 4Å: Chain B: Y.128, D.130, R.132, D.265, S.266, V.267, Q.272, A.275, I.279 Chain C: L.208, L.212, I.216, P.217, L.220, D.548, F.549 Ligands: POV.22 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:V.267, B:V.267, B:Q.272, B:I.279, C:L.208, C:I.216, C:I.216 Hydrogen bonds: B:V.267 Salt bridges: B:D.130, B:R.132 POV.22: 14 residues within 4Å: Chain B: R.132, W.133, Q.272, A.275, S.276, I.279, I.280, F.526, I.529, C.530, G.533, I.534, S.537 Ligands: POV.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.275, B:F.526 POV.25: 20 residues within 4Å: Chain B: I.279, G.282, L.283, V.286, I.290, Q.293, G.302, K.303 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 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.230, B:V.286, B:I.290 Salt bridges: C:R.517, C:R.517 Hydrogen bonds: B:Q.293 POV.28: 17 residues within 4Å: Chain C: Y.128, D.130, R.132, D.265, S.266, V.267, Q.272, A.275, I.279 Chain D: L.208, L.212, I.216, P.217, L.220, D.548, F.549 Ligands: POV.29 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:L.208, D:I.216, D:I.216, C:V.267, C:V.267, C:Q.272, C:I.279 Hydrogen bonds: C:V.267 Salt bridges: C:D.130, C:R.132 POV.29: 14 residues within 4Å: Chain C: R.132, W.133, Q.272, A.275, S.276, I.279, I.280, F.526, I.529, C.530, G.533, I.534, S.537 Ligands: POV.28 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.275, C:F.526 POV.32: 20 residues within 4Å: Chain C: I.279, G.282, L.283, V.286, I.290, Q.293, G.302, K.303 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 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.230, C:V.286, C:I.290 Salt bridges: D:R.517, D:R.517 Hydrogen bonds: C:Q.293 POV.35: 17 residues within 4Å: Chain D: Y.128, D.130, R.132, D.265, S.266, V.267, Q.272, A.275, I.279 Chain E: L.208, L.212, I.216, P.217, L.220, D.548, F.549 Ligands: POV.36 10 PLIP interactions: 3 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:L.208, E:I.216, E:I.216, D:V.267, D:V.267, D:Q.272, D:I.279 Hydrogen bonds: D:V.267 Salt bridges: D:D.130, D:R.132 POV.36: 14 residues within 4Å: Chain D: R.132, W.133, Q.272, A.275, S.276, I.279, I.280, F.526, I.529, C.530, G.533, I.534, S.537 Ligands: POV.35 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.275, D:F.526 POV.39: 20 residues within 4Å: Chain D: I.279, G.282, L.283, V.286, I.290, Q.293, G.302, K.303 Chain E: L.220, A.223, L.224, L.226, L.227, L.230, R.321, M.322, R.517, L.520, M.521, S.524 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.230, D:V.286, D:I.290 Salt bridges: E:R.517, E:R.517 Hydrogen bonds: D:Q.293 POV.42: 17 residues within 4Å: Chain A: L.208, L.212, I.216, P.217, L.220, D.548, F.549 Chain E: Y.128, D.130, R.132, D.265, S.266, V.267, Q.272, A.275, I.279 Ligands: POV.43 10 PLIP interactions: 7 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:V.267, E:V.267, E:Q.272, E:I.279, A:L.208, A:I.216, A:I.216 Hydrogen bonds: E:V.267 Salt bridges: E:D.130, E:R.132 POV.43: 14 residues within 4Å: Chain E: R.132, W.133, Q.272, A.275, S.276, I.279, I.280, F.526, I.529, C.530, G.533, I.534, S.537 Ligands: POV.42 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:A.275, E:F.526

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

9Z9.15: 9 residues within 4Å: Chain A: W.315, C.316, W.318, F.319, L.320, L.518, M.521, A.522, V.525 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.315, A:W.318, A:F.319, A:F.319, A:F.319, A:F.319, A:F.319, A:V.525 9Z9.23: 9 residues within 4Å: Chain B: W.315, C.316, W.318, F.319, L.320, L.518, M.521, A.522, V.525 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.315, B:W.318, B:F.319, B:F.319, B:F.319, B:F.319, B:F.319, B:V.525 9Z9.30: 9 residues within 4Å: Chain C: W.315, C.316, W.318, F.319, L.320, L.518, M.521, A.522, V.525 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.315, C:W.318, C:F.319, C:F.319, C:F.319, C:F.319, C:F.319, C:V.525 9Z9.37: 9 residues within 4Å: Chain D: W.315, C.316, W.318, F.319, L.320, L.518, M.521, A.522, V.525 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.315, D:W.318, D:F.319, D:F.319, D:F.319, D:F.319, D:F.319, D:V.525 9Z9.44: 9 residues within 4Å: Chain E: W.315, C.316, W.318, F.319, L.320, L.518, M.521, A.522, V.525 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:W.315, E:W.318, E:F.319, E:F.319, E:F.319, E:F.319, E:F.319, E:V.525

5 x EPJ: EPIBATIDINE(Non-covalent)

EPJ.16: 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: 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 Hydrogen bonds: C:Y.92, C:W.148 Water bridges: D:L.118 Halogen bonds: D:Q.116 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.45: 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: 3 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:W.54, 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

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 fusion: 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 fusion

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