Research workbench
Crystal structure of spectinomycin adenyltransferase AAD(9) from enterococcus faecialis with ATP and spectinomycin
Analyse Crystal structure of spectinomycin adenyltransferase AAD(9) from enterococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XXQ
- Type
- protein
- Length
- 496 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
- Q07448
- Ligands
- ATP, SCM, MG, NA
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Streptomycin 3''-adenylyltransferase (EC 2.7.7.47) | protein | 248 | 52% helix, 14% strand | Q07448 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- SCM · Spectinomycin · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.76 | 0.80 | 62 | NA, MG, ATP, SCM |
| 2 | 841 | 0.76 | 0.80 | 64 | NA, ATP, SCM |
| 3 | 90 | 0.34 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 296 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6XXQ · Crystal structure of spectinomycin adenyltransferase AAD(9) from Enterococcus faecialis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q07448 · AlphaFold monomer V2.0 prediction for spectinomycin 9-adenylyltransferase (Q07448) · a predicted model of the same protein · chain A 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 Q07448
- Elsewhere: RCSB PDB 6XXQ · PDBe 6XXQ · UniProt Q07448
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