Research workbench
Aada in complex with ATP, magnesium and streptomycin
Analyse Aada in complex with ATP, magnesium and streptomycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FZB
- Type
- protein
- Length
- 525 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptomycin 3''-adenylyltransferase
- EC
- 2.7.7.47
- UniProt
- Q8ZPX9
- Ligands
- SRY, ATP, MG, CL
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptomycin 3''-adenylyltransferase (EC 2.7.7.47) | protein | 262 | 52% helix, 13% strand | Q8ZPX9 |
| B | Streptomycin 3''-adenylyltransferase (EC 2.7.7.47) | protein | 263 | 53% helix, 13% strand | Q8ZPX9 |
Ligands and binding sites
- SRY · Streptomycin · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.74 | 0.80 | 57 | SRY, MG, ATP |
| 2 | 662 | 0.72 | 0.79 | 58 | SRY, MG, ATP |
| 3 | 50 | 0.47 | 0.85 | 14 | GOL |
| 4 | 57 | 0.38 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 485 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6FZB · AadA in complex with ATP, magnesium and streptomycin · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZPX9 · AlphaFold monomer V2.0 prediction for aminoglycoside (3'') (9) adenylyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8ZPX9
- Elsewhere: RCSB PDB 6FZB · PDBe 6FZB · UniProt Q8ZPX9
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