Research workbench
Crystal structure of aplysia achbp in complex with dmxba
Analyse Crystal structure of aplysia achbp in complex with dmxba in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WNJ
- Type
- protein
- Length
- 1,063 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- ZY7, NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 209 | 11% helix, 50% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 212 | 11% helix, 50% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 214 | 13% helix, 48% strand | Q8WSF8 |
| D | Soluble acetylcholine receptor | protein | 211 | 11% helix, 49% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 217 | 13% helix, 47% strand | Q8WSF8 |
Ligands and binding sites
- ZY7 · (3E)-3-[(2,4-dimethoxyphenyl)methylidene]-3,4,5,6-tetrahydro-2,3'-bipyridine · ligand · 5 copies · chains A, E, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.70 | 0.82 | 52 | ZY7 |
| 2 | 476 | 0.69 | 0.80 | 55 | ZY7 |
| 3 | 384 | 0.69 | 0.81 | 49 | ZY7 |
| 4 | 476 | 0.68 | 0.79 | 57 | ZY7 |
| 5 | 424 | 0.67 | 0.79 | 53 | ZY7 |
Interfaces
5 interfaces between chains.
- C–D · 1457 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1423 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1376 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1370 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1332 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 2WNJ · Crystal structure of aplysia achbp in complex with 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 2WNJ · PDBe 2WNJ · UniProt Q8WSF8
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