Research workbench
ROK repressor Lmo0178 from Listeria monocytogenes bound to inducer
Analyse ROK repressor Lmo0178 from Listeria monocytogenes bound to inducer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F7R
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
- Molecule
- Lmo0178 protein
- UniProt
- Q8YAF1
- Ligands
- GLC, ZN, CL, PO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.85 · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Lmo0178 protein | protein | 304 | 39% helix, 24% strand | Q8YAF1 |
| A | Lmo0178 protein | protein | 306 | 40% helix, 24% strand | Q8YAF1 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains E, A
- ZN · Zinc ion · metal · 2 copies · chains E, A
- CL · Chloride ion · ion · chains E, A
- PO4 · Phosphate ion · ion · chains E, A
- PEG · Di(hydroxyethyl)ether · additive · chains E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.69 | 0.81 | 56 | GLC |
| 2 | 318 | 0.68 | 0.83 | 52 | GLC |
| 3 | 97 | 0.38 | 0.75 | 15 | empty |
| 4 | 53 | 0.35 | 0.79 | 14 | PEG |
| 5 | 72 | 0.30 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- E–A · 1934 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5F7R · Rok repressor LMO0178 from listeria monocytogenes bound to inducer · 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 Q8YAF1
- Elsewhere: RCSB PDB 5F7R · PDBe 5F7R · UniProt Q8YAF1
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