MolNFT v1 · #119703 · protein
Aada in complex with ATP and magnesium
5G4A · Streptomycin 3''-adenylyltransferase: “Aada in complex with ATP and magnesium”. X-ray diffraction, 4 ligands (ATP, MG, UNK), 4 pockets (best druggability 0.75). MolNFT v1 #119703 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5G4A
- Type
- protein
- Length
- 523 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, MG, UNK, CL
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptomycin 3''-adenylyltransferase (EC 2.7.7.47) | protein | 261 | 54% helix, 13% strand | Q8ZPX9 |
| B | Streptomycin 3''-adenylyltransferase (EC 2.7.7.47) | protein | 262 | 54% helix, 13% strand | Q8ZPX9 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- UNK · Unknown · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains 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 | 718 | 0.75 | 0.80 | 60 | MG, ATP, UNK |
| 2 | 785 | 0.74 | 0.79 | 67 | ATP, UNK |
| 3 | 77 | 0.32 | 0.74 | 13 | empty |
| 4 | 80 | 0.31 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 422 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (artifact, oxidation).
Compared structures
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 5G4A · PDBe 5G4A · UniProt Q8ZPX9
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