MolNFT v1 · #155262 · protein
Cryo-EM structure of phosphorylated TYR39 a-synuclein amyloid fibril
6L1T · Alpha-synuclein: “Cryo-EM structure of phosphorylated TYR39 a-synuclein amyloid fibril”. Electron microscopy, 7 pockets (best druggability 0.76). MolNFT v1 #155262 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6L1T
- Type
- protein
- Length
- 1,000 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-synuclein
- UniProt
- P37840
- Pockets
- 7 · best druggability 0.76
Structure
electron microscopy · 1 distinct chain · 0% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Alpha-synuclein | protein | 100 | 0% helix, 50% strand | P37840 |
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.76 | 0.85 | 43 | empty |
| 2 | 478 | 0.73 | 0.83 | 43 | empty |
| 3 | 259 | 0.71 | 0.86 | 35 | empty |
| 4 | 243 | 0.71 | 0.86 | 35 | empty |
| 5 | 99 | 0.60 | 0.88 | 40 | empty |
Interfaces
19 interfaces between chains.
- D–E · 4029 Ų buried · 143 hydrogen bonds · protein-protein
- C–D · 3914 Ų buried · 114 hydrogen bonds · protein-protein
- G–H · 3907 Ų buried · 110 hydrogen bonds · protein-protein
- I–J · 3898 Ų buried · 103 hydrogen bonds · protein-protein
- B–C · 3890 Ų buried · 111 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (phosphorylation).
Compared structures
- 6L1T · Cryo-EM structure of phosphorylated Tyr39 a-synuclein amyloid fibril · 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 6L1T · PDBe 6L1T · UniProt P37840
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