MolNFT v1 · #176548 · protein
E. COLI gyrb ATPase domain in complex with methyl 2,4- dihydroxybenzoate
7DQF · DNA gyrase subunit B: “E. COLI gyrb ATPase domain in complex with methyl 2,4- dihydroxybenzoate”. X-ray diffraction, 3 ligands (HF9, AX7, PO4), 5 pockets (best druggability 0.62). MolNFT v1 #176548 on GenesisL1: 3D structure…
- PDB
- 7DQF
- Type
- protein
- Length
- 373 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
- HF9, AX7, PO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.6.2.2) | protein | 185 | 30% 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
- HF9 · methyl 2,4-bis(oxidanyl)benzoate · ligand · 2 copies · chains A, B
- AX7 · 1H-benzimidazol-2-amine · ligand · chains A, B
- PO4 · Phosphate ion · ion · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.62 | 0.82 | 26 | AX7 |
| 2 | 56 | 0.55 | 0.88 | 13 | HF9 |
| 3 | 66 | 0.49 | 0.84 | 16 | HF9 |
| 4 | 63 | 0.30 | 0.74 | 13 | empty |
| 5 | 51 | 0.28 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 464 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7DQF · E. coli GyrB ATPase domain in complex with methyl 2,4-dihydroxybenzoate · 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 7DQF · PDBe 7DQF · UniProt A0A4S5B230
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