SMTL ID : 8utb.1

Alpha7-nicotinic acetylcholine receptor bound to epibatidine and NS-1738

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: 5 residues within 4Å: Chain A: N.110, S.111, S.112, H.114 Chain E: K.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.114 NAG-NAG-BMA.4: 5 residues within 4Å: Chain A: K.191 Chain B: N.110, S.111, S.112, H.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.114 NAG-NAG-BMA.6: 5 residues within 4Å: Chain B: K.191 Chain C: N.110, S.111, S.112, H.114 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.114 NAG-NAG-BMA.8: 5 residues within 4Å: Chain C: K.191 Chain D: N.110, S.111, S.112, H.114 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.114 NAG-NAG-BMA.10: 5 residues within 4Å: Chain D: K.191 Chain E: N.110, S.111, S.112, H.114 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.114

5 x XG3: N-(5-chloro-2-hydroxyphenyl)-N'-[2-chloro-5-(trifluoromethyl)phenyl]urea(Non-covalent)

XG3.11: 19 residues within 4Å: Chain A: M.253, V.256, M.260, A.262, T.263, S.264, S.266, V.267, P.268, A.271, F.274, A.275, M.278 Chain B: L.208, Y.209, L.212, N.213, I.216, P.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.213 pi-Stacking: B:Y.209 XG3.17: 19 residues within 4Å: Chain B: M.253, V.256, M.260, A.262, T.263, S.264, S.266, V.267, P.268, A.271, F.274, A.275, M.278 Chain C: L.208, Y.209, L.212, N.213, I.216, P.217 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.213 pi-Stacking: C:Y.209 XG3.22: 19 residues within 4Å: Chain C: M.253, V.256, M.260, A.262, T.263, S.264, S.266, V.267, P.268, A.271, F.274, A.275, M.278 Chain D: L.208, Y.209, L.212, N.213, I.216, P.217 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.213 pi-Stacking: D:Y.209 XG3.27: 19 residues within 4Å: Chain D: M.253, V.256, M.260, A.262, T.263, S.264, S.266, V.267, P.268, A.271, F.274, A.275, M.278 Chain E: L.208, Y.209, L.212, N.213, I.216, P.217 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.213 pi-Stacking: E:Y.209 XG3.32: 19 residues within 4Å: Chain A: L.208, Y.209, L.212, N.213, I.216, P.217 Chain E: M.253, V.256, M.260, A.262, T.263, S.264, S.266, V.267, P.268, A.271, F.274, A.275, M.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.213 pi-Stacking: A:Y.209

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.70 NAG.18: 3 residues within 4Å: Chain B: N.67, S.69, E.70 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.70 NAG.23: 3 residues within 4Å: Chain C: N.67, S.69, E.70 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.70 NAG.28: 3 residues within 4Å: Chain D: N.67, S.69, E.70 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.70 NAG.33: 3 residues within 4Å: Chain E: N.67, S.69, E.70 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.70

5 x EPJ: EPIBATIDINE(Non-covalent)

EPJ.13: 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, T.105, N.106, L.108, Q.116, Y.117, L.118 7 PLIP interactions: 5 interactions with chain A, 2 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 EPJ.19: 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, T.105, N.106, L.108, Q.116, Y.117, L.118 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:W.54, C:L.118, B:Y.92, B:W.148, B:Y.187, B:Y.194 Hydrogen bonds: B:Y.92 EPJ.24: 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, T.105, N.106, L.108, Q.116, Y.117, L.118 7 PLIP interactions: 5 interactions with chain C, 2 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 EPJ.29: 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, T.105, N.106, L.108, Q.116, Y.117, L.118 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:Y.92, D:W.148, D:Y.187, D:Y.194, E:W.54, E:L.118 Hydrogen bonds: D:Y.92 EPJ.34: 15 residues within 4Å: Chain A: W.54, T.105, 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 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:W.54, A:L.118, E:Y.92, E:W.148, E:Y.187, E:Y.194 Hydrogen bonds: E:Y.92

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.320, L.518, M.521, A.522, V.525 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.315, A:W.315, A:F.319, A:F.319, A:F.319, A:F.319, A:A.522, A:V.525 9Z9.20: 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.315, B:F.319, B:F.319, B:F.319, B:F.319, B:A.522, B:V.525 9Z9.25: 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.315, C:F.319, C:F.319, C:F.319, C:F.319, C:A.522, C:V.525 9Z9.30: 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.315, D:F.319, D:F.319, D:F.319, D:F.319, D:A.522, D:V.525 9Z9.35: 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.315, E:F.319, E:F.319, E:F.319, E:F.319, E:A.522, E:V.525

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

POV.15: 22 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 Chain E: I.279, G.282, L.283, V.286, V.287, I.290, Q.293, H.297, G.302, K.303 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:L.283, E:V.286, E:V.286, A:L.220, A:A.223, A:L.227 Salt bridges: A:R.517 POV.16: 22 residues within 4Å: Chain A: I.279, G.282, L.283, V.286, V.287, I.290, Q.293, H.297, G.302, K.303 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 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.220, B:A.223, B:L.227, A:L.283, A:V.286, A:V.286 Salt bridges: B:R.517 POV.21: 22 residues within 4Å: Chain B: I.279, G.282, L.283, V.286, V.287, I.290, Q.293, H.297, G.302, K.303 Chain C: L.220, A.223, L.224, L.226, L.227, L.230, R.321, M.322, K.323, R.517, L.520, M.521 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.220, C:A.223, C:L.227, B:L.283, B:V.286, B:V.286 Salt bridges: C:R.517 POV.26: 22 residues within 4Å: Chain C: I.279, G.282, L.283, V.286, V.287, I.290, Q.293, H.297, G.302, K.303 Chain D: L.220, A.223, L.224, L.226, L.227, L.230, R.321, M.322, K.323, R.517, L.520, M.521 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.283, C:V.286, C:V.286, D:L.220, D:A.223, D:L.227 Salt bridges: D:R.517 POV.31: 22 residues within 4Å: Chain D: I.279, G.282, L.283, V.286, V.287, I.290, Q.293, H.297, G.302, K.303 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 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:L.283, D:V.286, D:V.286, E:L.220, E:A.223, E:L.227 Salt bridges: 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 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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