SMTL ID : 9dmq.1

Human muscle nAChR with fab3-bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.06 Å

Oligo State

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

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.1: 9 residues within 4Å: Chain A: N.161, S.163, W.204, K.205, H.206, S.207, T.222, H.224, V.226 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.207, A:H.206 NAG-NAG-BMA-MAN-MAN.7: 10 residues within 4Å: Chain E: W.159, N.161, S.163, V.213, R.215, I.231, S.233, I.235, P.483, L.485 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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.2: 9 residues within 4Å: Chain B: N.161, S.163, W.204, K.205, H.206, S.207, T.222, H.224, V.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.204, B:H.206

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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.3: 16 residues within 4Å: Chain C: W.162, N.164, T.166, R.216, I.218, P.221, I.236, Y.238, I.240, P.496, D.498, P.499, F.500, P.501, S.502, R.503 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.503, C:Y.238, C:P.501, C:R.503, C:R.503 Hydrophobic interactions: C:I.218, C:F.500 NAG-NAG-BMA-MAN-MAN-MAN.5: 14 residues within 4Å: Chain C: G.200 Chain D: W.162, N.164, S.166, R.219, N.221, P.224, R.225, Y.239, I.241, P.498, P.501, F.502, P.503 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.239, D:P.503

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 2 residues within 4Å: Chain D: N.190, R.191 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain E: R.43, Y.83, N.86, G.133, G.134 No protein-ligand interaction detected (PLIP)

1 x ACH: ACETYLCHOLINE(Non-covalent)

ACH.8: 11 residues within 4Å: Chain A: Y.113, T.168, W.169, T.170, Y.210, C.212, C.213, Y.218 Chain E: W.75, L.129, L.139 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:L.129 Water bridges: E:L.139 pi-Cation interactions: E:W.75, A:W.169, A:Y.210, A:Y.218

6 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 10 residues within 4Å: Chain A: L.232, V.236, I.240 Chain C: L.303, S.304, V.305, K.310, M.313, F.314, V.317 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:V.305, C:K.310, C:M.313, C:F.314, C:V.317, A:L.232, A:V.236 CLR.12: 11 residues within 4Å: Chain B: L.299, V.303, I.306, A.307, I.310 Chain D: L.247, I.250, I.251, V.255, L.259 Ligands: CLR.15 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:I.250, D:I.251, D:L.259, B:L.299, B:V.303, B:V.303, B:I.310 CLR.14: 10 residues within 4Å: Chain D: V.258, F.262, V.482, T.485, A.486, F.489, L.490, V.493, Y.494 Ligands: CLR.15 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.262, D:T.485, D:L.490, D:V.493, D:V.493 CLR.15: 11 residues within 4Å: Chain D: F.160, P.246, I.250, L.254, V.255, V.258, L.259, F.489, V.493 Ligands: CLR.12, CLR.14 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.160, D:F.160, D:I.250, D:I.250, D:L.254, D:V.255, D:F.489, D:V.493 CLR.17: 10 residues within 4Å: Chain E: T.153, Y.154, S.300, V.301, R.306, F.310, G.469, L.472, I.473 Ligands: CLR.18 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.153, E:I.473 CLR.18: 11 residues within 4Å: Chain B: L.232, V.236, I.240 Chain E: L.299, S.300, V.301, R.306, I.309, F.310, V.313 Ligands: CLR.17 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:V.301, E:I.309, E:V.313, B:L.232

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

POV.10: 15 residues within 4Å: Chain A: F.247, Y.254 Chain C: F.321, I.324, L.325, V.328, L.332, R.335, P.343, W.345, V.346, F.350, W.460, V.467, F.471 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.328, C:F.471 POV.13: 15 residues within 4Å: Chain C: L.261, F.265, Y.268 Chain D: M.322, V.325, I.326, I.329, I.333, R.336, S.344, V.347, F.351, W.462, V.465, V.469 13 PLIP interactions: 3 interactions with chain C, 10 interactions with chain D Hydrophobic interactions: C:F.265, C:F.265, D:M.322, D:V.325, D:I.329, D:I.329, D:I.329, D:I.333, D:V.347, D:F.351 Hydrogen bonds: C:Y.268 Salt bridges: D:R.336, D:R.336 POV.16: 17 residues within 4Å: Chain C: L.246, L.249, V.250, I.253, A.254, I.257, F.487 Chain D: T.156, M.304, A.305, I.306, K.311, L.314, F.315, V.318, L.319, M.322 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.306, D:K.311, D:L.314, D:F.315, D:V.318, D:L.319, C:I.253, C:A.254, C:I.257, C:F.487 Hydrogen bonds: D:I.306 POV.19: 25 residues within 4Å: Chain A: I.306, I.310, V.313, I.314, N.317, R.321, H.326 Chain E: V.252, L.253, G.256, L.257, L.259, L.260, Y.262, F.263, L.264, P.265, A.266, K.272, N.452, D.455, F.459, W.460, L.463, F.466 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain E Hydrophobic interactions: A:I.310, A:I.314, E:V.252, E:L.260, E:F.263, E:F.263, E:F.459, E:F.466 Hydrogen bonds: A:N.317 Salt bridges: A:H.326, E:D.455

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

NAG.11: 2 residues within 4Å: Chain D: E.93, N.97 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Structure of human muscle AChR with fab3-bound. To Be Published

Release Date

2025-04-09

Peptides

Acetylcholine receptor subunit alpha: AB
Acetylcholine receptor subunit beta: C
Acetylcholine receptor subunit delta: D
Acetylcholine receptor subunit epsilon: E
Fab3 heavy chain: F
Fab3 light chain: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
D

E
B

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 beta

Acetylcholine receptor subunit delta

Acetylcholine receptor subunit epsilon

Fab3 heavy chain

Fab3 light chain

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