Research workbench
Cryo-EM structure of bacteriophage Sf6 at 2.9 Angstrom resolution
Analyse Cryo-EM structure of bacteriophage Sf6 at 2.9 Angstrom resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L35
- Type
- protein
- Length
- 2,954 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.89
- Source
- Shigella phage Sf6
- Molecule
- Gene 5 protein
- UniProt
- Q716H0
- Ligands
- CL
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · resolution 2.89 · 1 distinct chain · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Gene 5 protein | protein | 422 | 19% helix, 33% strand | Q716H0 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.73 | 0.88 | 37 | empty |
| 2 | 63 | 0.72 | 0.97 | 20 | empty |
| 3 | 69 | 0.70 | 0.96 | 19 | empty |
| 4 | 334 | 0.66 | 0.81 | 56 | empty |
| 5 | 175 | 0.66 | 0.85 | 31 | empty |
Interfaces
8 interfaces between chains.
- B–C · 3430 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 3415 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 3409 Ų buried · 38 hydrogen bonds · protein-protein
- A–F · 3369 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3360 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5L35 · Cryo-EM structure of bacteriophage SF6 at 2.9 ångström resolution · 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 Q716H0
- Elsewhere: RCSB PDB 5L35 · PDBe 5L35 · UniProt Q716H0
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