Research workbench
S. aureus gyrase bound to an aminobenzimidazole urea inhibitor
Analyse S. aureus gyrase bound to an aminobenzimidazole urea inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P8O
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.99.1.3
- UniProt
- Q6GKU0
- Ligands
- 883
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 184 | 31% helix, 33% strand | Q6GKU0 |
Ligands and binding sites
- 883 · 1-ethyl-3-[5-(5-fluoropyridin-3-yl)-7-(pyrimidin-2-yl)-1H-benzimidazol-2-yl]urea · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.48 | 0.78 | 24 | 883 |
| 2 | 111 | 0.44 | 0.78 | 23 | 883 |
| 3 | 58 | 0.26 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 593 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 Q6GKU0
- Elsewhere: RCSB PDB 4P8O · PDBe 4P8O · UniProt Q6GKU0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.