MolNFT v1 · #141493 · protein
Bacterial gyrb ATPase domain in complex with (3,4-dichlorophenyl) hydrazine
5Z9B · DNA gyrase subunit B: “Bacterial gyrb ATPase domain in complex with (3,4-dichlorophenyl) hydrazine”. X-ray diffraction, 3 ligands (HX3, AX7, PO4), 4 pockets (best druggability 0.63). MolNFT v1 #141493 on GenesisL1: 3D structure…
- PDB
- 5Z9B
- 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
- 5.99.1.3
- UniProt
- P0AES6
- Ligands
- HX3, AX7, PO4
- Pockets
- 4 · 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 5.99.1.3) | protein | 186 | 30% helix, 30% strand | P0AES6 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 187 | 30% helix, 30% strand | P0AES6 |
Ligands and binding sites
- HX3 · (3,4-dichlorophenyl)hydrazine · ligand · 2 copies · chains A, B
- AX7 · 1H-benzimidazol-2-amine · ligand · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.63 | 0.82 | 29 | PO4, AX7 |
| 2 | 73 | 0.61 | 0.89 | 17 | HX3 |
| 3 | 72 | 0.57 | 0.88 | 16 | HX3 |
| 4 | 62 | 0.30 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 463 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5Z9B · Bacterial GyrB ATPase domain in complex with (3,4-dichlorophenyl)hydrazine · 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 A against A, TM-score 0.97
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 5Z9B · PDBe 5Z9B · UniProt P0AES6
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