Research workbench
Bacterial gyrb ATPase domain in complex with a chemical fragment
Analyse Bacterial gyrb ATPase domain in complex with a chemical fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z9Q
- Type
- protein
- Length
- 364 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
- P0AES6
- Ligands
- HX4, AX7, PO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 178 | 29% helix, 31% strand | P0AES6 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 186 | 30% helix, 31% strand | P0AES6 |
Ligands and binding sites
- HX4 · 5-phenyl-1H-pyrazol-3-amine · ligand · 2 copies · chains A, B
- AX7 · 1H-benzimidazol-2-amine · ligand · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.62 | 0.82 | 32 | PO4, AX7 |
| 2 | 134 | 0.55 | 0.82 | 24 | HX4 |
| 3 | 108 | 0.53 | 0.83 | 20 | HX4 |
| 4 | 50 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 465 Ų buried · 9 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 P0AES6
- Elsewhere: RCSB PDB 5Z9Q · PDBe 5Z9Q · UniProt P0AES6
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