MolNFT v1 · #114605 · protein
A receptor molecule
5BUO · Amyloid beta A4 protein: “A receptor molecule”. X-ray diffraction, 7 ligands (SGN, IDS, ZN), 1 pocket (best druggability 0.40). MolNFT v1 #114605 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BUO
- Type
- protein
- Length
- 197 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid beta A4 protein
- UniProt
- P05067
- Ligands
- SGN, IDS, ZN, CA, MG, SCN, SO4
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amyloid beta A4 protein | protein | 185 | 90% helix, 0% strand | P05067 |
| B | Amyloid beta A4 protein | protein | 12 | 33% helix, 0% strand | P05067 |
Ligands and binding sites
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar
- ZN · Zinc ion · metal · 6 copies · chains A
- CA · Calcium ion · metal
- MG · Magnesium ion · metal · chains A
- SCN · Thiocyanate ion · ion · 3 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.40 | 0.75 | 17 | ZN, SCN |
Interfaces
1 interface between chains.
- A–B · 233 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P05067
- Elsewhere: RCSB PDB 5BUO · PDBe 5BUO · UniProt P05067
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