Research workbench
Cryo-EM structure of alpha-synuclein fibril polymorph 2A
Analyse Cryo-EM structure of alpha-synuclein fibril polymorph 2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RT0
- Type
- protein
- Length
- 735 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-synuclein
- UniProt
- P37840
- Pockets
- 8 · best druggability 0.64
Structure
electron microscopy · 2 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Alpha-synuclein | protein | 74 | 0% helix, 53% strand | P37840 |
| F, G, H, I, J | Alpha-synuclein | protein | 73 | 0% helix, 52% strand | P37840 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.64 | 0.89 | 47 | empty |
| 2 | 110 | 0.62 | 0.88 | 48 | empty |
| 3 | 108 | 0.38 | 0.75 | 23 | empty |
| 4 | 82 | 0.34 | 0.75 | 23 | empty |
| 5 | 92 | 0.33 | 0.73 | 15 | empty |
Interfaces
19 interfaces between chains.
- B–C · 2899 Ų buried · 88 hydrogen bonds · protein-protein
- F–H · 2855 Ų buried · 82 hydrogen bonds · protein-protein
- D–E · 2838 Ų buried · 82 hydrogen bonds · protein-protein
- A–B · 2833 Ų buried · 82 hydrogen bonds · protein-protein
- A–D · 2819 Ų buried · 83 hydrogen bonds · protein-protein
Compared structures
- 6RT0 · cryo-em structure of alpha-synuclein fibril polymorph 2A · the same entry in another collection · chain A against A, 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 6RT0 · PDBe 6RT0 · UniProt P37840
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