MolNFT v1 · #125054 · protein
X-ray structure of the human ALPHA4BETA2 nicotinic receptor
5KXI · Neuronal acetylcholine receptor subunit alpha-4: “X-ray structure of the human ALPHA4BETA2 nicotinic receptor”. X-ray diffraction, 3 ligands (NCT, NAG, NA), 20 pockets (best druggability 0.78). MolNFT v1 #125054 on GenesisL1: 3D…
- PDB
- 5KXI
- Type
- protein
- Length
- 1,800 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuronal acetylcholine receptor subunit alpha-4; Neuronal acetylcholine receptor subunit…
- UniProt
- P43681, P17787
- Ligands
- NCT, NAG, NA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Neuronal acetylcholine receptor subunit alpha-4 | protein | 363 | 39% helix, 26% strand | P43681 |
| B, C, E | Neuronal acetylcholine receptor subunit beta-2 | protein | 358 | 37% helix, 27% strand | P17787 |
Ligands and binding sites
- NCT · (S)-3-(1-methylpyrrolidin-2-yl)pyridine · ligand · 2 copies · chains A, B, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D, E
- NA · Sodium ion · metal
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 | 1062 | 0.78 | 0.80 | 83 | NA |
| 2 | 393 | 0.72 | 0.83 | 50 | empty |
| 3 | 400 | 0.71 | 0.83 | 49 | empty |
| 4 | 419 | 0.71 | 0.82 | 58 | empty |
| 5 | 225 | 0.69 | 0.86 | 32 | empty |
Interfaces
5 interfaces between chains.
- D–E · 3021 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2989 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2700 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 2669 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 2559 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5KXI · X-ray structure of the human Alpha4Beta2 nicotinic receptor · the same entry in another collection · chain E against E, TM-score 1.00
- P43681 · AlphaFold monomer V2.0 prediction for neuronal acetylcholine receptor subunit alpha-4… · a predicted model of the same protein · chain D against A, TM-score 0.98
- P17787 · AlphaFold monomer V2.0 prediction for neuronal acetylcholine receptor subunit beta-2… · a predicted model of the same protein · chain B 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 P17787
- Elsewhere: RCSB PDB 5KXI · PDBe 5KXI · UniProt P43681 · UniProt P17787
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