Research workbench
E. COLI gyrb ATPase domain in complex with methyl 3,4- dihydroxybenzoate
Analyse E. COLI gyrb ATPase domain in complex with methyl 3,4- dihydroxybenzoate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DPR
- 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
- HE9, AX7, PO4
- Pockets
- 5 · best druggability 0.63
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 | 30% helix, 30% strand | A0A4S5B230 |
Ligands and binding sites
- HE9 · methyl 3,4-bis(oxidanyl)benzoate · ligand · 2 copies · chains A, B
- AX7 · 1H-benzimidazol-2-amine · ligand · chains A, B
- PO4 · Phosphate ion · ion · 5 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.63 | 0.82 | 28 | AX7, PO4 |
| 2 | 63 | 0.58 | 0.89 | 15 | HE9 |
| 3 | 64 | 0.56 | 0.88 | 14 | HE9 |
| 4 | 69 | 0.31 | 0.74 | 14 | empty |
| 5 | 56 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 473 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7DPR · E. coli GyrB ATPase domain in complex with methyl 3,4-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 7DPR · PDBe 7DPR · UniProt A0A4S5B230
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