Research workbench
Human ALPHA3BETA4 nicotinic acetylcholine receptor in complex with at- 1001
Analyse Human ALPHA3BETA4 nicotinic acetylcholine receptor in complex with at- 1001 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PV8
- Type
- protein
- Length
- 2,379 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion protein of neuronal acetylcholine receptor subunit alpha-3 and soluble cytochrome…
- UniProt
- P32297, A0A3W4NZ06, P30926
- Ligands
- Y01, P1M, NAG, MAN, BMA, NA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fusion protein of neuronal acetylcholine receptor subunit alpha-3 and soluble cytochrome B562 | protein | 387 | 36% helix, 24% strand | P32297, A0A3W4NZ06 |
| B, E | Fusion protein of neuronal acetylcholine receptor subunit beta-4 and soluble cytochrome B562 | protein | 388 | 38% helix, 22% strand | A0A3W4NZ06, P30926 |
| C | Fusion protein of neuronal acetylcholine receptor subunit beta-4 and soluble cytochrome B562 | protein | 385 | 36% helix, 21% strand | A0A3W4NZ06, P30926 |
| F, H | IGG2B Fab heavy chain | protein | 117 | 3% helix, 48% strand | — |
| G, I | Kappa Fab light chain | protein | 105 | 0% helix, 46% strand | — |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 10 copies · chains A, E, B, C, D
- P1M · (3-endo)-N-(2-bromophenyl)-9-methyl-9-azabicyclo[3.3.1]nonan-3-amine · ligand · 2 copies · chains A, B, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B, H, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains A, C, D, E
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, D
- NA · Sodium ion · metal · chains A, B, C, 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.82 | 0.83 | 104 | NA |
| 2 | 659 | 0.76 | 0.82 | 86 | empty |
| 3 | 162 | 0.74 | 0.91 | 24 | P1M |
| 4 | 168 | 0.74 | 0.91 | 23 | P1M |
| 5 | 836 | 0.74 | 0.78 | 49 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3520 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 3471 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 3154 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 3089 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 2442 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 11 disulfide (N-glycosylation, disulfide).
Compared structures
- 6PV8 · Human alpha3beta4 nicotinic acetylcholine receptor in complex with AT-1001 · the same entry in another collection · chain I against I, TM-score 1.00
- P32297 · AlphaFold monomer V2.0 prediction for neuronal acetylcholine receptor subunit alpha-3… · a predicted model of the same protein · chain D against A, TM-score 0.98
- P30926 · AlphaFold monomer V2.0 prediction for neuronal acetylcholine receptor subunit beta-4… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P32297
- Every structure of UniProt A0A3W4NZ06
- Every structure of UniProt P30926
- Elsewhere: RCSB PDB 6PV8 · PDBe 6PV8 · UniProt P32297 · UniProt A0A3W4NZ06 · UniProt P30926
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