Research workbench
Crystal structure of Staphylococcus aureus Gyrase B co-complexed with 4-METHYL-5-[3-(METHYLSULFANYL)-1H-PYRAZOL-5-YL]-2-THIOPHEN-2-YL-1,3-THIAZOLE inhibitor
Analyse Crystal structure of Staphylococcus aureus Gyrase B co-complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G75
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Staphylococcus aureus
- Molecule
- DNA gyrase subunit B
- EC
- 5.99.1.3
- UniProt
- P0A0K8
- Ligands
- B48
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · resolution 2.3 · 1 distinct chain · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 184 | 28% helix, 32% strand | P0A0K8 |
Ligands and binding sites
- B48 · 4-methyl-5-[3-(methylsulfanyl)-1H-pyrazol-5-yl]-2-thiophen-2-yl-1,3-thiazole · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.54 | 0.79 | 21 | B48 |
| 2 | 123 | 0.49 | 0.79 | 23 | B48 |
Interfaces
1 interface between chains.
- A–B · 552 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3G75 · Crystal structure of staphylococcus aureus gyrase B co-complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A0K8 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0A0K8) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0A0K8
- Elsewhere: RCSB PDB 3G75 · PDBe 3G75 · UniProt P0A0K8
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