Research workbench
Cryoem structure of human ALPHA4BETA2 nicotinic acetylcholine receptor with varenicline in complex with anti-bril synthetic antibody BAK5
Analyse Cryoem structure of human ALPHA4BETA2 nicotinic acetylcholine receptor with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6USF
- Type
- protein
- Length
- 2,868 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera of soluble cytochrome B562 (bril) and neuronal acetylcholine receptor subunit…
- UniProt
- P43681, P0ABE7, P17787
- Ligands
- QMR, NAG, BMA
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 7 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Chimera of soluble cytochrome B562 (bril) and neuronal acetylcholine receptor subunit alpha-4 | protein | 464 | 36% helix, 19% strand | P43681, P0ABE7 |
| B | Neuronal acetylcholine receptor subunit beta-2 | protein | 358 | 30% helix, 25% strand | P17787 |
| C, E | Neuronal acetylcholine receptor subunit beta-2 | protein | 357 | 29% helix, 25% strand | P17787 |
| H | Fab heavy chain | protein | 219 | 5% helix, 47% strand | — |
| L | Fab light chain | protein | 209 | 7% helix, 46% strand | — |
| K | Fab heavy chain | protein | 227 | 6% helix, 48% strand | — |
| M | Fab light chain | protein | 213 | 4% helix, 47% strand | — |
Ligands and binding sites
- QMR · Varenicline · ligand · 2 copies · chains A, B, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, C, E, A, D
- BMA · beta-D-mannopyranose · sugar · 3 copies
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 | 1070 | 0.78 | 0.79 | 94 | empty |
| 2 | 1147 | 0.77 | 0.79 | 117 | empty |
| 3 | 687 | 0.73 | 0.79 | 68 | empty |
| 4 | 623 | 0.71 | 0.79 | 59 | empty |
| 5 | 245 | 0.70 | 0.85 | 32 | QMR |
Interfaces
11 interfaces between chains.
- A–B · 2873 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 2818 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 2772 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 2719 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 2238 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6USF · CryoEM structure of human alpha4beta2 nicotinic acetylcholine receptor with varenicline… · the same entry in another collection · chain M against M, TM-score 1.00
- P17787 · AlphaFold monomer V2.0 prediction for neuronal acetylcholine receptor subunit beta-2… · a predicted model of the same protein · chain E 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 P43681
- Every structure of UniProt P0ABE7
- Every structure of UniProt P17787
- Elsewhere: RCSB PDB 6USF · PDBe 6USF · UniProt P43681 · UniProt P0ABE7 · UniProt P17787
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