Research workbench
Positively supercharged variant of the computationally designed cage protein O3-33
Analyse Positively supercharged variant of the computationally designed cage protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FDB
- Type
- protein
- Length
- 1,472 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.619
- Source
- Salmonella choleraesuis
- Molecule
- Propanediol utilization protein
- UniProt
- A0A0M0QF47
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · resolution 3.619 · 1 distinct chain · 40% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Propanediol utilization protein | protein | 184 | 40% helix, 32% strand | A0A0M0QF47 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.56 | 0.79 | 29 | empty |
| 2 | 220 | 0.55 | 0.78 | 28 | empty |
| 3 | 160 | 0.55 | 0.81 | 29 | empty |
| 4 | 196 | 0.54 | 0.78 | 26 | empty |
| 5 | 125 | 0.50 | 0.80 | 27 | empty |
Interfaces
12 interfaces between chains.
- G–H · 911 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 876 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 875 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 810 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 477 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6FDB · Positively supercharged variant of the computationally designed cage protein O3-33 · 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 A0A0M0QF47
- Elsewhere: RCSB PDB 6FDB · PDBe 6FDB · UniProt A0A0M0QF47
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