Research workbench
Cryo-EM structure of phosphorylated Tyr39 alpha-synuclein amyloid fibril
Analyse Cryo-EM structure of phosphorylated Tyr39 alpha-synuclein amyloid fibril in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L1U
- Type
- protein
- Length
- 1,500 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.37
- Molecule
- Alpha-synuclein
- UniProt
- P37840
- Pockets
- 9 · best druggability 0.75
Structure
electron microscopy · resolution 3.37 · 1 distinct chain · 0% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O | Alpha-synuclein | protein | 100 | 0% helix, 54% strand | P37840 |
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.75 | 0.82 | 39 | empty |
| 2 | 577 | 0.73 | 0.81 | 41 | empty |
| 3 | 566 | 0.73 | 0.81 | 43 | empty |
| 4 | 242 | 0.69 | 0.85 | 34 | empty |
| 5 | 234 | 0.68 | 0.85 | 34 | empty |
Interfaces
39 interfaces between chains.
- I–J · 3976 Ų buried · 129 hydrogen bonds · protein-protein
- D–E · 3964 Ų buried · 129 hydrogen bonds · protein-protein
- N–O · 3953 Ų buried · 129 hydrogen bonds · protein-protein
- B–C · 3944 Ų buried · 126 hydrogen bonds · protein-protein
- M–N · 3938 Ų buried · 123 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (phosphorylation).
Compared structures
- 6L1U · Cryo-EM structure of phosphorylated TYR39 alpha-synuclein amyloid fibril · the same entry in another collection · chain O against O, 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 P37840
- Elsewhere: RCSB PDB 6L1U · PDBe 6L1U · UniProt P37840
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