MolNFT v1 · #168999 · protein
X-ray crystallographic structure of a beta-hairpin peptide derived from amyloid beta 16-36
6WXM · Amyloid-beta protein: “X-ray crystallographic structure of a beta-hairpin peptide derived from amyloid beta 16-36”. X-ray diffraction, 6 pockets (best druggability 0.65). MolNFT v1 #168999 on GenesisL1: 3D structure, binding sites…
- PDB
- 6WXM
- Type
- protein
- Length
- 242 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid-beta protein
- UniProt
- P05067
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, H, B, I, E, A, C, D, J, G, K | Amyloid-beta protein | protein | 22 | 0% helix, 59% strand | P05067 |
Ligands and binding sites
- HEZ · Hexane-1,6-diol · additive · 10 copies · chains F, H, B, A, G, I, E, K, C, D, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.65 | 0.75 | 50 | HEZ |
| 2 | 162 | 0.62 | 0.84 | 26 | HEZ |
| 3 | 321 | 0.60 | 0.77 | 34 | empty |
| 4 | 180 | 0.58 | 0.81 | 27 | HEZ |
| 5 | 167 | 0.45 | 0.75 | 24 | empty |
Interfaces
25 interfaces between chains.
- H–G · 373 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 372 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 361 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 359 Ų buried · 7 hydrogen bonds · protein-protein
- F–E · 357 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 modified, 11 disulfide (nonstandard, disulfide, methylation).
Compared structures
- 6WXM · X-ray crystallographic structure of a beta-hairpin peptide derived from amyloid beta 16-36 · the same entry in another collection · chain K against K, TM-score 1.00
- 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 0.34
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 6WXM · PDBe 6WXM · UniProt P05067
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.