4PDQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Synthesis, broad spectrum antibacterial activity, and X-ray co-crystal structure of the decoding bacterial ribosomal A-site with 4'-deoxy-4'-fluoro neomycin analogs

Hanessian, S.Saavedra, O.M.Vilchis-Reyes, M.A.Maianti, J.P.Kanazawa, H.Dozzo, P.Matias, R.D.Serio, A.Kondo, J.

(2014) Chem Sci 5: 4621-4632


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
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')A,B23synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NMZ
Query on NMZ

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Download CCD File 
B
(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
1-N-[(S)-4-Amino-2-hydroxybutanoyl]-4'-deoxy-4'-fluoro-4'-epineomycin
C27 H52 F N7 O14
VWXJAOATJPQONW-MKAHEPKYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 103.657α = 90.00
b = 103.657β = 90.00
c = 44.572γ = 120.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXmodel building
CrystalCleardata scaling
CrystalCleardata reduction
PDB_EXTRACTdata extraction
CNSrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-07
    Type: Initial release