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CryoEM structures of amplified alpha-synuclein fibril class B type II with extended core from DLB case I
Analyse CryoEM structures of amplified alpha-synuclein fibril class B type II with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CYS
- Type
- protein
- Length
- 1,008 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Homo sapiens
- Molecule
- Alpha-synuclein
- UniProt
- P37840
- Pockets
- 6 · best druggability 0.82
Structure
electron microscopy · resolution 3.1 · 1 distinct chain · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L, I, B, J, C, K, D, E, M, F, N, G, O | Alpha-synuclein | protein | 72 | 0% helix, 51% strand | P37840 |
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 | 957 | 0.82 | 0.84 | 81 | empty |
| 2 | 964 | 0.82 | 0.83 | 87 | empty |
| 3 | 134 | 0.73 | 0.92 | 36 | empty |
| 4 | 137 | 0.73 | 0.92 | 37 | empty |
| 5 | 73 | 0.29 | 0.73 | 25 | empty |
Interfaces
30 interfaces between chains.
- L–M · 2839 Ų buried · 78 hydrogen bonds · protein-protein
- I–J · 2837 Ų buried · 78 hydrogen bonds · protein-protein
- N–O · 2837 Ų buried · 78 hydrogen bonds · protein-protein
- L–K · 2836 Ų buried · 78 hydrogen bonds · protein-protein
- M–N · 2836 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- P37840 · AlphaFold monomer V2.0 prediction for alpha-synuclein (P37840) · a predicted model of the same protein · chain A against A, TM-score 0.21
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 P37840
- Elsewhere: RCSB PDB 8CYS · PDBe 8CYS · UniProt P37840
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