Research workbench

Torpedo muscle-type nicotinic acetylcholine receptor - nicotine-bound conformation

Analyse Torpedo muscle-type nicotinic acetylcholine receptor - nicotine-bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QL5
Type: protein
Length: 1,989 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetylcholine receptor subunit alpha; Acetylcholine receptor subunit beta; Acetylcholine…
UniProt: P02710, P02712, P02718, P02714
Ligands: POV, NCT, MAN, NAG, BMA
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 5 distinct chains · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetylcholine receptor subunit alpha	protein	390	42% helix, 23% strand	P02710
B	Acetylcholine receptor subunit beta	protein	399	38% helix, 24% strand	P02712
C	Acetylcholine receptor subunit delta	protein	423	38% helix, 25% strand	P02718
D	Acetylcholine receptor subunit alpha	protein	371	40% helix, 23% strand	P02710
E	Acetylcholine receptor subunit gamma	protein	406	39% helix, 25% strand	P02714

Ligands and binding sites

POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 11 copies · chains A, E, B, C, D
NCT · (S)-3-(1-methylpyrrolidin-2-yl)pyridine · ligand · 2 copies · chains A, E, C, D
MAN · alpha-D-mannopyranose · sugar · 16 copies · chains A, E, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, C, D, E
BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	956	0.85	0.86	82	empty
2	484	0.69	0.80	54	empty
3	375	0.68	0.81	51	empty
4	505	0.67	0.78	42	empty
5	185	0.66	0.86	27	empty

Interfaces

5 interfaces between chains.

C–D · 3205 Å² buried · 25 hydrogen bonds · protein-protein
A–E · 3138 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 3095 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 3056 Å² buried · 32 hydrogen bonds · protein-protein
D–E · 2813 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan, 7 disulfide (N-glycosylation, disulfide).

Compared structures

7QL5 · Torpedo muscle-type nicotinic acetylcholine receptor - nicotine-bound conformation · the same entry in another collection · chain E against E, TM-score 1.00
P02712 · AlphaFold monomer V2.0 prediction for acetylcholine receptor subunit beta (P02712) · a predicted model of the same protein · chain B against A, TM-score 0.99
P02714 · AlphaFold monomer V2.0 prediction for acetylcholine receptor subunit gamma (P02714) · a predicted model of the same protein · chain E against A, TM-score 0.99
P02718 · AlphaFold monomer V2.0 prediction for acetylcholine receptor subunit delta (P02718) · a predicted model of the same protein · chain C against A, TM-score 0.98
P02710 · AlphaFold monomer V2.0 prediction for acetylcholine receptor subunit alpha (P02710) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P02710
Every structure of UniProt P02712
Every structure of UniProt P02718
Every structure of UniProt P02714
Elsewhere: RCSB PDB 7QL5 · PDBe 7QL5 · UniProt P02710 · UniProt P02712 · UniProt P02718 · UniProt P02714

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