Research workbench
Crystal structure of aplysia achbp in complex with 4-0H-dmxba
Analyse Crystal structure of aplysia achbp in complex with 4-0H-dmxba in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WN9
- Type
- protein
- Length
- 1,053 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- ZY5, NAG, MAN, BMA
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 209 | 10% helix, 50% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 211 | 11% helix, 53% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 214 | 12% helix, 49% strand | Q8WSF8 |
| D | Soluble acetylcholine receptor | protein | 205 | 11% helix, 51% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 214 | 14% helix, 52% strand | Q8WSF8 |
Ligands and binding sites
- ZY5 · 4-[(E)-5,6-dihydro-2,3'-bipyridin-3(4H)-ylidenemethyl]-3-methoxyphenol · ligand · 5 copies · chains A, E, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.71 | 0.81 | 58 | ZY5 |
| 2 | 479 | 0.70 | 0.80 | 66 | ZY5 |
| 3 | 583 | 0.70 | 0.78 | 62 | ZY5 |
| 4 | 472 | 0.66 | 0.78 | 44 | ZY5 |
| 5 | 501 | 0.65 | 0.77 | 64 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1374 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1353 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1353 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1306 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1303 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2WN9 · Crystal structure of Aplysia ACHBP in complex with 4-0H-DMXBA · 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
- Every structure of UniProt Q8WSF8
- Elsewhere: RCSB PDB 2WN9 · PDBe 2WN9 · UniProt Q8WSF8
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