Research workbench
Mycobacterium smegmatis gyrb 22KDA ATPase sub-domain in complex with novobiocin
Analyse Mycobacterium smegmatis gyrb 22KDA ATPase sub-domain in complex with novobiocin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y8O
- Type
- protein
- Length
- 374 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
- P0C559
- Ligands
- NOV, NA
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.6.2.2) | protein | 188 | 35% helix, 30% strand | P0C559 |
| B | DNA gyrase subunit B (EC 5.6.2.2) | protein | 186 | 33% helix, 30% strand | P0C559 |
Ligands and binding sites
- NOV · Novobiocin · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- ACT · Acetate ion · additive · 3 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.77 | 0.80 | 110 | EDO, NA |
| 2 | 122 | 0.50 | 0.80 | 22 | NOV |
| 3 | 112 | 0.44 | 0.78 | 22 | NOV |
Interfaces
1 interface between chains.
- A–B · 609 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6Y8O · Mycobacterium smegmatis GyrB 22kDa ATPase sub-domain in complex with novobiocin · 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 6Y8O · PDBe 6Y8O · UniProt P0C559
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.