Research workbench
Crystal structure of gyraseb N-terminal at 1.93A resolution
Analyse Crystal structure of gyraseb N-terminal at 1.93A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZXM
- Type
- protein
- Length
- 780 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.6.2.2
- UniProt
- A0A3R0U328
- Ligands
- ADP, MG, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA gyrase subunit B (EC 5.6.2.2) | protein | 390 | 37% helix, 25% strand | A0A3R0U328 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.81 | 0.98 | 33 | ADP, MG |
| 2 | 146 | 0.80 | 0.97 | 30 | ADP |
| 3 | 782 | 0.73 | 0.78 | 78 | empty |
| 4 | 180 | 0.54 | 0.79 | 22 | empty |
| 5 | 55 | 0.38 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2857 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 5ZXM · Crystal Structure of GyraseB N-terminal at 1.93A Resolution · 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 A0A3R0U328
- Elsewhere: RCSB PDB 5ZXM · PDBe 5ZXM · UniProt A0A3R0U328
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