› 2g5k

X-ray diffraction
2.8Å resolution

Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with Apramycin

Released:
DOI: 10.2210/pdb2g5k/pdb
PDB entry 2g5k coloured by chain, front view.
PDB entry 2g5k coloured by chain, side view.
PDB entry 2g5k coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding site complexed with apramycin.
Kondo J, François B, Urzhumtsev A, Westhof E
Angew Chem Int Ed Engl 45 3310-4 (2006)
PMID: 16596680

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-196362 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3' Chains: A, B
Molecule details ›
Chains: A, B
Length: 23 nucleotides
Theoretical weight: 7.36 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P31
Unit cell:
a: 33.123Å b: 33.123Å c: 116.421Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.258 0.258 0.27
Expression system: Not provided

Quick links

Citations

7 review citations

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Šponer et al. (2018)
6 more

3 mentions without citation

Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots.
Bindewald et al. (2011)
2 more