Research workbench
Cryo-EM structure of human AA amyloid fibril
Analyse Cryo-EM structure of human AA amyloid fibril in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MST
- Type
- protein
- Length
- 648 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens
- Molecule
- Serum amyloid A-1 protein
- UniProt
- P0DJI8
- Pockets
- 10 · best druggability 0.73
Structure
electron microscopy · resolution 2.7 · 1 distinct chain · 0% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, D, F, H, I, J, K, L, G | Serum amyloid A-1 protein | protein | 54 | 0% helix, 46% strand | P0DJI8 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.73 | 0.90 | 34 | empty |
| 2 | 204 | 0.73 | 0.89 | 36 | empty |
| 3 | 122 | 0.64 | 0.88 | 27 | empty |
| 4 | 121 | 0.62 | 0.87 | 29 | empty |
| 5 | 59 | 0.51 | 0.86 | 23 | empty |
Interfaces
45 interfaces between chains.
- A–C · 2557 Ų buried · 76 hydrogen bonds · protein-protein
- I–K · 2552 Ų buried · 73 hydrogen bonds · protein-protein
- J–L · 2544 Ų buried · 72 hydrogen bonds · protein-protein
- B–D · 2537 Ų buried · 72 hydrogen bonds · protein-protein
- I–G · 2536 Ų buried · 73 hydrogen bonds · protein-protein
Compared structures
- 6MST · Cryo-EM structure of human aa amyloid fibril · the same entry in another collection · chain L against L, 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 P0DJI8
- Elsewhere: RCSB PDB 6MST · PDBe 6MST · UniProt P0DJI8
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