Research workbench
Humanized alpha-achbp (acetylcholine binding protein) in complex with lobeline and allosteric binder fragment 4.
Analyse Humanized alpha-achbp (acetylcholine binding protein) in complex with lobeline… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OUG
- Type
- protein
- Length
- 1,025 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Humanized alpha-achbp
- Ligands
- 9Z0, L0B, NAG, BMA, MAN
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Humanized alpha-achbp | protein | 205 | 8% helix, 54% strand | — |
Ligands and binding sites
- 9Z0 · 4,5-dibromo-N-(3-hydroxypropyl)-1H-pyrrole-2-carboxamide · ligand · 10 copies · chains A, B, C, D, E
- L0B · Alpha-Lobeline · ligand · 5 copies · chains A, E, B, C, D
- 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
- DMS · Dimethyl sulfoxide · additive · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.72 | 0.78 | 75 | L0B |
| 2 | 546 | 0.71 | 0.80 | 59 | 9Z0 |
| 3 | 678 | 0.71 | 0.78 | 75 | L0B |
| 4 | 561 | 0.70 | 0.79 | 58 | L0B |
| 5 | 510 | 0.69 | 0.79 | 57 | L0B |
Interfaces
5 interfaces between chains.
- C–D · 1249 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1231 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1227 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1224 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1214 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5OUG · Humanized alpha-AChBP (acetylcholine binding protein) in complex with lobeline and… · 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 5OUG · PDBe 5OUG
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