Research workbench
Cryoem tetra protofilament structure of the hamster prion 108-144 fibril
Analyse Cryoem tetra protofilament structure of the hamster prion 108-144 fibril in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YAT
- Type
- protein
- Length
- 600 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major prion protein
- UniProt
- P04273
- Pockets
- 12 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 0% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, X, Y | Major prion protein | protein | 25 | 0% helix, 60% strand | P04273 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.80 | 0.91 | 47 | empty |
| 2 | 279 | 0.79 | 0.90 | 47 | empty |
| 3 | 281 | 0.78 | 0.90 | 46 | empty |
| 4 | 279 | 0.78 | 0.89 | 48 | empty |
| 5 | 78 | 0.67 | 0.92 | 24 | empty |
Interfaces
64 interfaces between chains.
- B–C · 986 Ų buried · 38 hydrogen bonds · protein-protein
- S–Y · 983 Ų buried · 35 hydrogen bonds · protein-protein
- T–U · 981 Ų buried · 33 hydrogen bonds · protein-protein
- M–R · 975 Ų buried · 33 hydrogen bonds · protein-protein
- A–F · 965 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 7YAT · CryoEM tetra protofilament structure of the hamster prion 108-144 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 P04273
- Elsewhere: RCSB PDB 7YAT · PDBe 7YAT · UniProt P04273
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