Research workbench
Aiifl segment derived from ALZHEIMER'S amyloid-beta displayed on 42- membered macrocycle scaffold
Analyse Aiifl segment derived from ALZHEIMER'S amyloid-beta displayed on 42- membered… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q9J
- Type
- protein
- Length
- 64 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
- Ligands
- HAO, ORN, ZN, CL
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN) | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- HAO · {[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo) acetic acid · ligand · 8 copies · chains A, G, H, B, C, D, E, F
- ORN · L-ornithine · ligand · 8 copies · chains A, D, B, C, E, H, F, G
- ZN · Zinc ion · metal · 8 copies · chains A, D, H, B, C, G, E, F
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D, E, G, F, H
- GOL · Glycerol · additive · 3 copies · chains B, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
16 interfaces between chains.
- E–F · 266 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 248 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 246 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 233 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 177 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 covalent, 8 modified (covalent ligand, nonstandard).
Compared structures
- 3Q9J · AIIFL segment derived from Alzheimer's Amyloid-Beta displayed on 42-membered macrocycle… · the same entry in another collection · chain F against F, 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 3Q9J · PDBe 3Q9J
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.