MolNFT v1 · #147776 · protein
Crystal structure of the 43K ATPase domain of escherichia COLI gyrase B in complex with an aminocoumarin
6ENG · DNA gyrase subunit B: “Crystal structure of the 43K ATPase domain of escherichia COLI gyrase B in complex with an aminocoumarin”. X-ray diffraction, 5 ligands (BHW, K, NA), 7 pockets (best druggability 0.74). MolNFT v1 #147776 on…
- PDB
- 6ENG
- Type
- protein
- Length
- 750 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.99.1.3
- UniProt
- P0AES6
- Ligands
- BHW, K, NA, PO4, CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 371 | 36% helix, 25% strand | P0AES6 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 379 | 37% helix, 25% strand | P0AES6 |
Ligands and binding sites
- BHW · Coumermycin A1 · ligand · chains A, B
- K · Potassium ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.74 | 0.89 | 30 | BHW |
| 2 | 343 | 0.69 | 0.82 | 52 | BHW |
| 3 | 302 | 0.62 | 0.79 | 33 | NA, K |
| 4 | 244 | 0.60 | 0.80 | 31 | empty |
| 5 | 108 | 0.42 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 73 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ENG · Crystal structure of the 43K ATPase domain of Escherichia coli gyrase B in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AES6 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0AES6) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 6ENG · PDBe 6ENG · UniProt P0AES6
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