Research workbench
Hfq from E.coli with inserted long loop L4 sequence
Analyse Hfq from E.coli with inserted long loop L4 sequence in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XYJ
- Type
- protein
- Length
- 481 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.772
- Source
- Pseudomonas aeruginosa (strain PA7)
- Molecule
- RNA-binding protein Hfq
- UniProt
- A6VD57
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.772 · 3 distinct chains · 16% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA, DDD, EEE, FFF | RNA-binding protein Hfq | protein | 80 | 16% helix, 51% strand | A6VD57 |
| BBB | RNA-binding protein Hfq | protein | 82 | 16% helix, 51% strand | A6VD57 |
| CCC | RNA-binding protein Hfq | protein | 79 | 16% helix, 53% strand | A6VD57 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.72 | 0.76 | 60 | empty |
| 2 | 54 | 0.32 | 0.76 | 14 | empty |
| 3 | 52 | 0.28 | 0.75 | 11 | empty |
| 4 | 51 | 0.27 | 0.74 | 13 | empty |
Interfaces
6 interfaces between chains.
- BBB–EEE · 923 Ų buried · 17 hydrogen bonds · protein-protein
- AAA–BBB · 869 Ų buried · 12 hydrogen bonds · protein-protein
- CCC–FFF · 848 Ų buried · 13 hydrogen bonds · protein-protein
- CCC–DDD · 779 Ų buried · 12 hydrogen bonds · protein-protein
- AAA–DDD · 743 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- A6VD57 · AlphaFold monomer V2.0 prediction for RNA-binding protein hfq (A6VD57) · a predicted model of the same protein · chain EEE against A, TM-score 0.82
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 A6VD57
- Elsewhere: RCSB PDB 6XYJ · PDBe 6XYJ · UniProt A6VD57
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.