SMTL ID : 8v8d.1

Alpha7-nicotinic acetylcholine receptor time resolved bound to epibatidine and PNU-120596 asymmetric state 2

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: 7 residues within 4Å: Chain A: Y.31, N.110, S.111, S.112, H.114, Q.116 Chain E: K.191 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 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.3: 6 residues within 4Å: Chain B: K.191 Chain C: Y.31, N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 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.5: 5 residues within 4Å: Chain D: K.191 Chain E: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain A: N.67, S.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.67, A:S.69 NAG.7: 3 residues within 4Å: Chain A: N.23, S.25, Q.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.26 NAG.12: 3 residues within 4Å: Chain B: N.67, S.69, E.70 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.67, B:S.69, B:E.70 NAG.13: 3 residues within 4Å: Chain B: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain C: N.67, S.69 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.69 NAG.18: 3 residues within 4Å: Chain C: N.23, S.25, Q.26 No protein-ligand interaction detected (PLIP) NAG.22: 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.23: 3 residues within 4Å: Chain D: N.23, S.25, Q.26 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.23 NAG.26: 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 NAG.27: 3 residues within 4Å: Chain E: N.23, S.25, Q.26 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.26

5 x EPJ: EPIBATIDINE(Non-covalent)

EPJ.8: 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 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.92, A:W.148, A:Y.187, A:Y.194, B:W.54, B:Q.116, B:L.118 Hydrogen bonds: A:Y.92, A:Y.92 Halogen bonds: B:Q.116 EPJ.14: 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 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:Y.187, B:Y.194 Hydrogen bonds: B:Y.92, B:Y.92 EPJ.19: 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 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.92, C:Y.187, C:Y.194, D:W.54, D:L.118 Hydrogen bonds: C:Y.92, C:Y.92 EPJ.24: 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 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:Y.92, D:Y.187, D:Y.194, E:W.54, E:L.118, E:L.118 Hydrogen bonds: D:Y.92, D:Y.92 EPJ.28: 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 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:Y.92, E:Y.187, E:Y.194, A:W.54, A:L.118 Hydrogen bonds: E:Y.92, E:Y.92

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

I34.9: 18 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, P.268, A.271, Q.272, A.275, M.278 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.217, A:F.252 Hydrogen bonds: A:N.213, A:N.213 I34.10: 17 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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.217 Hydrogen bonds: B:N.213, B:N.213, B:N.213 I34.15: 17 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 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:P.217, B:M.253 Hydrogen bonds: C:N.213, C:N.213 I34.20: 17 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 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.212, D:P.217, D:F.252 Hydrogen bonds: D:N.213, D:N.213 I34.25: 16 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, P.217, I.221, V.251, F.252, L.255 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:V.267, E:F.252 Hydrogen bonds: E:N.213, E:N.213, E:N.213

3 x CA: CALCIUM ION(Non-covalent)

CA.11: 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.16: 3 residues within 4Å: Chain B: A.262 Chain C: E.172, Y.210 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.172 CA.21: 6 residues within 4Å: Chain D: V.42, D.43, E.44, R.205, Y.210, I.259 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.44, D:E.44

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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