› 2ogn

X-ray diffraction
3.56Å resolution

The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080

Released:
DOI: 10.2210/pdb2ogn/pdb
PDB 2ogn coloured by chain and viewed from the front.
PDB 2ogn coloured by chain and viewed from the side.
PDB 2ogn coloured by chain and viewed from the top.
Source organism: Deinococcus radiodurans
Primary publication:
Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.
Davidovich C, Bashan A, Auerbach-Nevo T, Yaggie RD, Gontarek RR, Yonath A
Proc. Natl. Acad. Sci. U.S.A. 104 4291-6 (2007)
PMID: 17360517

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
50S ribosomal protein L3 Chain: B
Molecule details ›
Chain: B
Length: 211 amino acids
Theoretical weight: 22.48 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXK2 (Residues: 1-211; Coverage: 100%)
Gene names: DR_0311, rplC
Sequence domains: Ribosomal protein L3
23S ribosomal RNA Chain: 0
Molecule details ›
Chain: 0
Length: 2880 nucleotides
Theoretical weight: 933.41 KDa
Source organism: Deinococcus radiodurans
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand G80 1 x G80
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: I222
Unit cell:
a: 170.475Å b: 412.738Å c: 696.67Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.276 0.276 0.338

Quick links

Citations

27 review citations

ABC-F translation factors: from antibiotic resistance to immune response.
Fostier et al. (2021)
26 more

3 mentions without citation

Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.
Davidovich et al. (2007)
2 more