Research workbench
Crystal structure of the 43K ATPase domain of thermus thermophilus gyrase B in complex with novobiocin
Analyse Crystal structure of the 43K ATPase domain of thermus thermophilus gyrase B in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KIJ
- Type
- protein
- Length
- 768 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
- Q9LCX5
- Ligands
- NOV
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 384 | 38% helix, 27% strand | Q9LCX5 |
Ligands and binding sites
- NOV · Novobiocin · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.88 | 0.91 | 110 | NOV |
| 2 | 159 | 0.70 | 0.89 | 26 | empty |
| 3 | 168 | 0.49 | 0.77 | 36 | empty |
| 4 | 53 | 0.28 | 0.74 | 12 | empty |
| 5 | 50 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2266 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1KIJ · Crystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex… · 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 Q9LCX5
- Elsewhere: RCSB PDB 1KIJ · PDBe 1KIJ · UniProt Q9LCX5
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