Research workbench
Ecoli GYRB24 with inhibitor 16A
Analyse Ecoli GYRB24 with inhibitor 16A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YD9
- Type
- protein
- Length
- 198 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.6.2.2
- UniProt
- P0AES6
- Ligands
- ON2
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.6.2.2) | protein | 198 | 34% helix, 29% strand | P0AES6 |
Ligands and binding sites
- ON2 · N-[6-(3-azanylpropanoylamino)-1,3-benzothiazol-2-yl]-3, 4-bis(chloranyl)-5-methyl-1H-pyrrole-2-carboxamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.52 | 0.80 | 28 | ON2 |
| 2 | 59 | 0.41 | 0.81 | 13 | empty |
Compared structures
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 6YD9 · PDBe 6YD9 · UniProt P0AES6
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