Research workbench
E. COLI gyrb ATPase domain in complex with naringenin
Analyse E. COLI gyrb ATPase domain in complex with naringenin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DQM
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.6.2.2
- UniProt
- A0A4S5B230
- Ligands
- AX7, CWE, PO4
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.6.2.2) | protein | 196 | 29% helix, 30% strand | A0A4S5B230 |
| B | DNA gyrase subunit B (EC 5.6.2.2) | protein | 188 | 29% helix, 30% strand | A0A4S5B230 |
Ligands and binding sites
- AX7 · 1H-benzimidazol-2-amine · ligand · chains A, B
- CWE · R-naringenin · ligand · chains B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.63 | 0.82 | 29 | AX7 |
| 2 | 64 | 0.48 | 0.84 | 14 | CWE |
| 3 | 133 | 0.45 | 0.77 | 25 | empty |
| 4 | 50 | 0.32 | 0.78 | 15 | empty |
| 5 | 62 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 475 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7DQM · E. coli GyrB ATPase domain in complex with Naringenin · 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 A0A4S5B230
- Elsewhere: RCSB PDB 7DQM · PDBe 7DQM · UniProt A0A4S5B230
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