MolNFT v1 · #156360 · protein
The DNA gyrase B ATP binding domain of pseudomonas aeruginosa in complex with compound 12X
6M1J · DNA gyrase subunit B: “The DNA gyrase B ATP binding domain of pseudomonas aeruginosa in complex with compound 12X”. X-ray diffraction, 3 ligands (EZ6, NA, SO4), 3 pockets (best druggability 0.57). MolNFT v1 #156360 on GenesisL1: 3D…
- PDB
- 6M1J
- Type
- protein
- Length
- 376 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
- Q9I7C2
- Ligands
- EZ6, NA, SO4
- Pockets
- 3 · best druggability 0.57
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 5.6.2.2) | protein | 189 | 30% helix, 29% strand | Q9I7C2 |
| B | DNA gyrase subunit B (EC 5.6.2.2) | protein | 187 | 30% helix, 30% strand | Q9I7C2 |
Ligands and binding sites
- EZ6 · 1-[5-[6-fluoranyl-8-(methylamino)-4-[3-(trifluoromethyl)pyrazol-1-yl]-9H-pyrido[2,3-b]indol-3-yl]pyrimidin-2-yl]cyclopropane-1-carboxylic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.57 | 0.77 | 38 | EZ6 |
| 2 | 105 | 0.48 | 0.81 | 23 | EZ6 |
| 3 | 198 | 0.46 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 548 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6M1J · The DNA Gyrase B ATP binding domain of PSEUDOMONAS AERUGINOSA in complex with compound 12x · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I7C2 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (Q9I7C2) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9I7C2
- Elsewhere: RCSB PDB 6M1J · PDBe 6M1J · UniProt Q9I7C2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.