Research workbench
De novo designed octahedral nanoparticle O43_dn18
Analyse De novo designed octahedral nanoparticle O43_dn18 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VFI
- Type
- protein
- Length
- 315 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.54
- Source
- synthetic construct
- Molecule
- O43_dn18B; O43_dn18A
- Pockets
- 1 · best druggability 0.30
Structure
electron microscopy · resolution 4.54 · 2 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | O43_dn18B | protein | 118 | 79% helix, 0% strand | — |
| A | O43_dn18A | protein | 197 | 83% helix, 0% strand | — |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.30 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 696 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6VFI · De novo designed octahedral nanoparticle O43_DN18 · 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
- Elsewhere: RCSB PDB 6VFI · PDBe 6VFI
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