SMTL ID : 8yqn.1

Torpedo acetylcholine receptor in complex with Erabutoxin A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1: 11 residues within 4Å: Chain A: N.141, W.184, K.185, H.186, W.187, Y.189, T.202, H.204, I.206 Chain F: Q.7, E.38 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.184, A:T.202 Hydrogen bonds: A:H.186 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2: 10 residues within 4Å: Chain D: N.141, W.184, K.185, H.186, W.187, Y.189, T.202, H.204 Chain G: Q.7, E.38 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.184 Hydrogen bonds: D:H.186

2 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.3: 8 residues within 4Å: Chain B: W.141, N.143, N.200, Y.218, P.482, P.485, F.486, E.487 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.487 NAG-NAG-BMA.4: 7 residues within 4Å: Chain C: W.139, N.141, R.194, N.196, Y.210, P.467, F.468 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.194, C:R.194, C:N.196, C:Y.210

1 x NAG- NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-MAN-MAN.5: 9 residues within 4Å: Chain E: W.139, N.141, K.192, W.197, F.212, P.479, F.480, P.481, G.482 No protein-ligand interaction detected (PLIP)

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

POV.6: 11 residues within 4Å: Chain A: L.231, Y.234, F.326, S.327, T.328, H.408, M.415, L.416 Chain E: M.299, R.310 Ligands: PLM.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.231, A:Y.234, A:M.415, A:L.416 Hydrogen bonds: A:Y.234 POV.10: 6 residues within 4Å: Chain C: V.277, R.282, M.285, F.286, I.289, I.454 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.454 POV.11: 9 residues within 4Å: Chain B: F.312, R.315, H.320 Chain C: I.233, L.237, Y.240, W.331, Q.333, R.437 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.237, C:Y.240, C:Y.240, B:F.312 Hydrogen bonds: C:Y.240 Salt bridges: C:R.437, B:R.315 POV.12: 10 residues within 4Å: Chain C: F.293, I.296, R.307, W.317 Chain D: Y.234, F.326, S.327, T.328, H.408, M.415 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.293, C:I.296, D:Y.234 Salt bridges: C:R.307 Hydrogen bonds: D:Y.234, D:F.326, D:T.328

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

NAG.7: 3 residues within 4Å: Chain B: N.70, S.72, E.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.70, B:E.73 NAG.8: 3 residues within 4Å: Chain B: F.206, N.208 Chain C: Q.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.208 NAG.13: 3 residues within 4Å: Chain E: N.68, S.70, E.71 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.71

1 x OCT: N-OCTANE(Non-functional Binders)

OCT.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x PLM: PALMITIC ACID(Covalent)

PLM.14: 6 residues within 4Å: Chain E: N.300, R.310, I.321, W.440, C.451 Ligands: POV.6 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.321, E:W.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, C.Y.L. et al., Structure of Erabutoxin bound to Torpedo acetylcholine receptor gives insight to intramolecular selectivity. To Be Published

Release Date

2025-05-28

Peptides

Acetylcholine receptor subunit alpha: AD
Acetylcholine receptor subunit delta: B
Acetylcholine receptor subunit beta: C
Acetylcholine receptor subunit gamma: E
Erabutoxin a: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

E
E

F
F

G
G

Membrane

We predict this structure to be a membrane protein.
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Acetylcholine receptor subunit alpha

Acetylcholine receptor subunit delta

Acetylcholine receptor subunit beta

Acetylcholine receptor subunit gamma

Erabutoxin a

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