Research workbench
Crystal structures of the ligand binding domain of a pentameric ALPHA7 nicotinic receptor chimera with its agonist epibatidine
Analyse Crystal structures of the ligand binding domain of a pentameric ALPHA7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SQ6
- Type
- protein
- Length
- 2,030 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuronal acetylcholine receptor subunit alpha-7, acetylcholine-binding protein
- Ligands
- EPJ, NAG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, I | Neuronal acetylcholine receptor subunit alpha-7, acetylcholine-binding protein | protein | 204 | 7% helix, 47% strand | — |
| C, H | Neuronal acetylcholine receptor subunit alpha-7, acetylcholine-binding protein | protein | 203 | 7% helix, 48% strand | — |
| E, F, G, J | Neuronal acetylcholine receptor subunit alpha-7, acetylcholine-binding protein | protein | 202 | 7% helix, 49% strand | — |
Ligands and binding sites
- EPJ · Epibatidine · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains I, A, B, C, D, E, F, G, H
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 | 997 | 0.75 | 0.78 | 75 | empty |
| 2 | 363 | 0.68 | 0.81 | 43 | EPJ |
| 3 | 370 | 0.68 | 0.81 | 43 | EPJ |
| 4 | 373 | 0.68 | 0.81 | 43 | EPJ |
| 5 | 378 | 0.68 | 0.81 | 40 | EPJ |
Interfaces
14 interfaces between chains.
- H–I · 1461 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1455 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1445 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1433 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1424 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 3SQ6 · Crystal Structures of the Ligand Binding Domain of a Pentameric Alpha7 Nicotinic Receptor… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3SQ6 · PDBe 3SQ6
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