› 2oe5

X-ray diffraction
1.51Å resolution

1.5 A X-ray crystal structure of Apramycin complex with RNA fragment GGCGUCGCUAGUACCG/GGUACUAAAAGUCGCCC containing the human ribosomal decoding A site: RNA construct with 3'-overhang

Released:
DOI: 10.2210/pdb2oe5/pdb
PDB entry 2oe5 coloured by chain, front view.
PDB entry 2oe5 coloured by chain, side view.
PDB entry 2oe5 coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Apramycin recognition by the human ribosomal decoding site.
Hermann T, Tereshko V, Skripkin E, Patel DJ
Blood Cells Mol Dis 38 193-8
PMID: 17258916

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-196547 (preferred)
Entry contents:
2 distinct RNA molecules
Macromolecules (2 distinct):
RNA (5'-R(*GP*GP*CP*GP*UP*CP*GP*CP*UP*AP*GP*UP*AP*CP*CP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 16 nucleotides
Theoretical weight: 5.13 KDa
Source organism: Synthetic construct
Expression system: Not provided
RNA (5'-R(*GP*GP*UP*AP*CP*UP*AP*AP*AP*AP*GP*UP*CP*GP*CP*CP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 17 nucleotides
Theoretical weight: 5.43 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand SO4 1 x SO4
Ligand MG 2 x MG
Ligand AM2 1 x AM2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X9A
Spacegroup: P212121
Unit cell:
a: 28.31Å b: 36.693Å c: 86.679Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.199 0.227
Expression system: Not provided

Quick links

Citations

5 review citations

Antibiotics that target protein synthesis.
McCoy et al. (2011)
4 more

6 mentions without citation

Aminoglycoside multiacetylating activity of the enhanced intracellular survival protein from Mycobacterium smegmatis and its inhibition.
Chen et al. (2012)
5 more