Research workbench
Cryo-EM structure of the fibril formed by disaccharide-modified amyloid-BETA(1-42)
Analyse Cryo-EM structure of the fibril formed by disaccharide-modified… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F29
- Type
- protein
- Length
- 222 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid-beta A4 protein
- UniProt
- B4DM00
- Ligands
- X6X, GAL
- Pockets
- 2 · best druggability 0.51
Structure
electron microscopy · 1 distinct chain · 0% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, C, D, F, A, B | Amyloid-beta A4 protein | protein | 37 | 0% helix, 65% strand | B4DM00 |
Ligands and binding sites
- X6X · 2-amino-2-deoxy-alpha-D-galactopyranose · ligand · 6 copies · chains E, C, D, F, A, B
- GAL · beta-D-galactopyranose · sugar · 6 copies
- ACY · Acetic acid · additive · 6 copies · chains E, C, D, F, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.51 | 0.84 | 18 | empty |
| 2 | 83 | 0.50 | 0.83 | 20 | empty |
Interfaces
9 interfaces between chains.
- F–B · 1498 Ų buried · 41 hydrogen bonds · protein-protein
- E–C · 1494 Ų buried · 42 hydrogen bonds · protein-protein
- F–A · 1493 Ų buried · 41 hydrogen bonds · protein-protein
- E–D · 1491 Ų buried · 41 hydrogen bonds · protein-protein
- D–F · 84 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7F29 · Cryo-EM structure of the fibril formed by disaccharide-modified amyloid-beta(1-42) · the same entry in another collection · chain E against E, 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
- Every structure of UniProt B4DM00
- Elsewhere: RCSB PDB 7F29 · PDBe 7F29 · UniProt B4DM00
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