Research workbench
The DNA gyrase B ATP binding domain of escherichia COLI in complex with a small molecule inhibitor.
Analyse The DNA gyrase B ATP binding domain of escherichia COLI in complex with a small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KFG
- Type
- protein
- Length
- 380 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
- DOO, SO4
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 189 | 30% helix, 30% strand | P0AES6 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 191 | 30% helix, 28% strand | P0AES6 |
Ligands and binding sites
- DOO · 6-fluoro-4-[(3aR,6aR)-hexahydropyrrolo[3,4-b]pyrrol-5(1H)-yl]-N-methyl-2-[(2-methylpyrimidin-5-yl)oxy]-9H-pyrimido[4,5-b]indol-8-amine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.65 | 0.77 | 68 | DOO |
| 2 | 319 | 0.65 | 0.81 | 36 | DOO |
| 3 | 211 | 0.49 | 0.75 | 32 | SO4 |
Interfaces
1 interface between chains.
- A–B · 484 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4KFG · The DNA Gyrase B ATP binding domain of Escherichia coli in complex with a small molecule… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AES6 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0AES6) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 4KFG · PDBe 4KFG · UniProt P0AES6
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