MolNFT v1 · #86427 · protein
Structure of the M. smegmatis gyrb ATPase domain in complex with an aminopyrazinamide
4B6C · DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase…: “Structure of the M. smegmatis gyrb ATPase domain in complex with an aminopyrazinamide”. X-ray diffraction, 2 ligands (B5U, NA), 3 pockets (best druggability 0.61). MolNFT v1…
- PDB
- 4B6C
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit B
- EC
- 5.99.1.3
- UniProt
- P0C559
- Ligands
- B5U, NA
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 161 | 27% helix, 34% strand | P0C559 |
| B | DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 167 | 26% helix, 34% strand | P0C559 |
Ligands and binding sites
- B5U · 6-(3,4-dimethylphenyl)-3-[[4-[3-(4-methylpiperazin-1-yl)propoxy]phenyl]amino]pyrazine-2-carboxamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.61 | 0.80 | 27 | B5U |
| 2 | 140 | 0.55 | 0.82 | 19 | B5U |
| 3 | 57 | 0.36 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 616 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4B6C · Structure of the M. smegmatis GyrB ATPase domain in complex with an aminopyrazinamide · the same entry in another collection · chain A against A, TM-score 1.00
- P0C559 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0C559) · a predicted model of the same protein · chain B 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 P0C559
- Elsewhere: RCSB PDB 4B6C · PDBe 4B6C · UniProt P0C559
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