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Structure of the M. smegmatis gyrb ATPase domain in complex with an aminopyrazinamide
Analyse Structure of the M. smegmatis gyrb ATPase domain in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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