MolNFT v2 · #216432 · protein
Hexameric Hfq from Chromobacterium haemolyticum
8P9M · RNA-binding protein Hfq: “Hexameric Hfq from Chromobacterium haemolyticum”. X-ray diffraction at 2, 1 pocket (best druggability 0.69). MolNFT v2 #216432 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8P9M
- Type
- protein
- Length
- 410 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Chromobacterium haemolyticum
- Molecule
- RNA-binding protein Hfq
- UniProt
- A0A1W0CX06
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · resolution 2 · 5 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA-binding protein Hfq | protein | 66 | 20% helix, 47% strand | A0A1W0CX06 |
| B | RNA-binding protein Hfq | protein | 73 | 18% helix, 42% strand | A0A1W0CX06 |
| D | RNA-binding protein Hfq | protein | 68 | 19% helix, 44% strand | A0A1W0CX06 |
| E | RNA-binding protein Hfq | protein | 67 | 19% helix, 46% strand | A0A1W0CX06 |
| F | RNA-binding protein Hfq | protein | 70 | 19% helix, 43% strand | A0A1W0CX06 |
Ligands and binding sites
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.69 | 0.75 | 62 | empty |
Interfaces
6 interfaces between chains.
- A–B · 888 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 874 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 872 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 860 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 774 Ų buried · 10 hydrogen bonds · protein-protein
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 A0A1W0CX06
- Elsewhere: RCSB PDB 8P9M · PDBe 8P9M · UniProt A0A1W0CX06
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