SMTL ID : 8cau.1

human alpha7 nicotinic receptor in complex with the C4 nanobody and nicotine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-mer

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: 4 residues within 4Å: Chain A: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: N.110, S.111, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: 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.23, S.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.25 NAG.7: 3 residues within 4Å: Chain A: N.67, S.69, E.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.67 NAG.9: 2 residues within 4Å: Chain B: N.23, S.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.25 NAG.10: 3 residues within 4Å: Chain B: N.67, S.69, E.70 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.67 NAG.12: 2 residues within 4Å: Chain C: N.23, S.25 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.25, C:Q.26 NAG.13: 3 residues within 4Å: Chain C: N.67, S.69, E.70 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.67 NAG.15: 3 residues within 4Å: Chain D: N.23, S.25, Q.26 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.25, D:Q.26 NAG.16: 3 residues within 4Å: Chain D: N.67, S.69, E.70 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.67 NAG.18: 2 residues within 4Å: Chain E: N.23, S.25 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.25 NAG.19: 3 residues within 4Å: Chain E: N.67, S.69, E.70 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.67

5 x NCT: (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE(Non-covalent)

NCT.8: 11 residues within 4Å: Chain A: Y.92, S.147, W.148, Y.187, C.189, C.190, Y.194 Chain B: W.54, L.108, Q.116, L.118 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.54, B:L.118 pi-Cation interactions: A:W.148, A:W.148, A:Y.187 NCT.11: 10 residues within 4Å: Chain B: Y.92, S.147, W.148, Y.187, C.189, C.190, Y.194 Chain C: W.54, L.108, L.118 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C pi-Cation interactions: B:W.148, B:W.148 Hydrophobic interactions: C:W.54, C:L.118 NCT.14: 11 residues within 4Å: Chain C: Y.92, S.147, W.148, Y.187, C.189, C.190, Y.194 Chain D: W.54, L.108, Q.116, L.118 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.54 NCT.17: 10 residues within 4Å: Chain D: Y.92, S.147, W.148, Y.187, C.189, C.190, Y.194 Chain E: W.54, L.108, L.118 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.148 pi-Cation interactions: D:Y.194 NCT.20: 10 residues within 4Å: Chain A: W.54, L.108, L.118 Chain E: Y.92, S.147, W.148, Y.187, C.189, C.190, Y.194 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.148 pi-Cation interactions: E:Y.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prevost, M.S. et al., An original potentiating mechanism revealed by the cryo-EM structures of the human alpha 7 nicotinic receptor in complex with nanobodies. Nat Commun (2023)

Release Date

2023-10-11

Peptides

Neuronal acetylcholine receptor subunit alpha-7: ABCDE
Nanobody C4: FGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Neuronal acetylcholine receptor subunit alpha-7

Nanobody C4

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