Research workbench
Humanized alpha-achbp (acetylcholine binding protein) in complex with allosteric binder fragment CU2017
Analyse Humanized alpha-achbp (acetylcholine binding protein) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OUI
- Type
- protein
- Length
- 1,025 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine binding protein
- Ligands
- AVB, NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Acetylcholine binding protein | protein | 205 | 10% helix, 48% strand | — |
Ligands and binding sites
- AVB · (3~{R})-~{N}-(5-bromanylpyridin-2-yl)piperidine-3-carboxamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- EDO · 1,2-ethanediol · additive · 26 copies · chains A, B, E, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.77 | 0.79 | 83 | PEG, EDO |
| 2 | 1127 | 0.77 | 0.79 | 101 | empty |
| 3 | 953 | 0.77 | 0.79 | 86 | EDO |
| 4 | 926 | 0.76 | 0.79 | 86 | EDO |
| 5 | 580 | 0.69 | 0.78 | 55 | EDO |
Interfaces
5 interfaces between chains.
- C–D · 1240 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1237 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1229 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1226 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1207 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5OUI · Humanized alpha-AChBP (acetylcholine binding protein) in complex with allosteric binder… · 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 5OUI · PDBe 5OUI
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