Research workbench
Aada E87Q in complex with ATP, calcium and dihydrostreptomycin
Analyse Aada E87Q in complex with ATP, calcium and dihydrostreptomycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LPA
- Type
- protein
- Length
- 534 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
- ATP, 71R, CA, CL
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Streptomycin 3''-adenylyltransferase (EC 2.7.7.47) | protein | 267 | 54% helix, 13% strand | Q8ZPX9 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- 71R · dihydrostreptomycin · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.74 | 0.78 | 74 | ATP, 71R, CA |
| 2 | 788 | 0.74 | 0.78 | 67 | ATP, 71R, CA |
| 3 | 62 | 0.29 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 329 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 5LPA · AadA E87Q in complex with ATP, calcium and dihydrostreptomycin · 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 0.97
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 Q8ZPX9
- Elsewhere: RCSB PDB 5LPA · PDBe 5LPA · UniProt Q8ZPX9
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