› 1jzx

X-ray diffraction
3.1Å resolution

Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria

Released:
DOI: 10.2210/pdb1jzx/pdb
PDB 1jzx coloured by chain and viewed from the front.
PDB 1jzx coloured by chain and viewed from the side.
PDB 1jzx coloured by chain and viewed from the top.
Source organism: Deinococcus radiodurans
Primary publication:
Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria.
Schlünzen F, Zarivach R, Harms J, Bashan A, Tocilj A, Albrecht R, Yonath A, Franceschi F
Nature 413 814-21 (2001)
PMID: 11677599

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
3 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
50S ribosomal protein L4 Chain: K
Molecule details ›
Chain: K
Length: 205 amino acids
Theoretical weight: 22.31 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXK1 (Residues: 1-205; Coverage: 100%)
Gene names: DR_0312, rplD
50S ribosomal protein L22 Chain: L
Molecule details ›
Chain: L
Length: 134 amino acids
Theoretical weight: 15.19 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ7 (Residues: 1-134; Coverage: 100%)
Gene names: DR_0316, rplV
50S ribosomal protein L32 Chain: M
Molecule details ›
Chain: M
Length: 60 amino acids
Theoretical weight: 6.81 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: P49228 (Residues: 1-60; Coverage: 100%)
Gene names: DR_2366, rpmF
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2880 nucleotides
Theoretical weight: 933.41 KDa
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand CLY 1 x CLY
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: I222
Unit cell:
a: 170.3Å b: 410.1Å c: 697.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.273 0.268 0.303

Quick links

Citations

118 review citations

Targeted antibiotic discovery through biosynthesis-associated resistance determinants: target directed genome mining.
O'Neill et al. (2019)
117 more

12 mentions without citation

The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning.
Wilson et al. (2008)
11 more