4PDQ: Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neomycin analog

PDB ID: 4PDQDownload
MMDB ID: 125904
PDB Deposition Date: 2014/4/21
Updated in MMDB: 2020/01
Experimental Method:
x-ray diffraction
Resolution: 3  Å
Source Organism:
Biological Unit for 4PDQ: dimeric; determined by author and by software (PISA)
Molecular Components in 4PDQ
Label Count Molecule
Nucleotides(2 molecules)
2
RNA (5'-*up*up*gp*cp*gp*up*cp*ap*cp*gp*cp*cp*gp*gp*cp*gp*ap*ap*gp*up*cp*gp*c-3')
Molecule annotation
Chemicals and Non-standard biopolymers (3 molecules)
1
2
MAGNESIUM IONMAGNESIUM ION
2
1
(2S)-4-amino-N-{(1R,2S,3R,4R,5S)-5-amino-3-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-4-[(2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranosyl)oxy]-2-hydroxycyclohexyl}-2-hydroxybutanamide(2S)-4-amino-N-{(1R,2S,3R,4R,5S)-5-amino-3-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-4-[(2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranosyl)oxy]-2-hydroxycyclohexyl}-2-hydroxybutanamide
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303