Research workbench
S. aureus gyrb ATPase domain in complex with a small molecule inhibitor
Analyse S. aureus gyrb ATPase domain in complex with a small molecule inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U2K
- Type
- protein
- Length
- 379 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
- P0A0K8
- Ligands
- 087, MG
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 194 | 35% helix, 30% strand | P0A0K8 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 185 | 34% helix, 32% strand | P0A0K8 |
Ligands and binding sites
- 087 · 2-chloro-6-(4-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}piperidin-1-yl)pyridine-4-carboxamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.51 | 0.79 | 26 | 087, MG |
| 2 | 131 | 0.49 | 0.79 | 21 | 087 |
| 3 | 172 | 0.48 | 0.76 | 20 | empty |
| 4 | 54 | 0.28 | 0.75 | 14 | empty |
| 5 | 56 | 0.25 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 282 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3U2K · S. aureus GyrB ATPase domain in complex with a small molecule inhibitor · 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 B 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 3U2K · PDBe 3U2K · UniProt P0A0K8
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