MolNFT v1 · #97132 · protein
The DNA gyrase B ATP binding domain of enterococcus faecalis in complex with a small molecule inhibitor
4K4O · DNA gyrase subunit B: “The DNA gyrase B ATP binding domain of enterococcus faecalis in complex with a small molecule inhibitor”. X-ray diffraction, 1 ligand (DOO), 1 pocket (best druggability 0.50). MolNFT v1 #97132 on GenesisL1: 3D…
- PDB
- 4K4O
- Type
- protein
- Length
- 190 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.99.1.3
- UniProt
- Q839Z1
- Ligands
- DOO
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 190 | 31% helix, 31% strand | Q839Z1 |
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 · chains A
- TBU · Tertiary-butyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.50 | 0.82 | 17 | DOO |
Compared structures
- 4K4O · The DNA Gyrase B ATP binding domain of Enterococcus faecalis in complex with a small… · the same entry in another collection · chain A against A, TM-score 1.00
- Q839Z1 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (Q839Z1) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q839Z1
- Elsewhere: RCSB PDB 4K4O · PDBe 4K4O · UniProt Q839Z1
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