1O9M

THE COMPLEX OF A NOVEL ANTIBIOTIC WITH THE AMINOACYL SITE OF THE BACTERIAL RIBOSOME REVEALED BY X-RAY CRYSTALLOGRAPHY.

Structural Biology Knowledgebase: 1O9M SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.298
  • R-Value Work: 0.251

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1O9M

Classification: ANTIBIOTIC / RNA

Total Structure Weight: 14671.33

Macromolecule Entities
Molecule Chains Length Organism Details
EUBACTERIAL A-SITE A, B 22 Escherichia coli

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BDG
Query on BDG

B O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE
C6 H14 N2 O4
SQTHUUHOUPJYLK-UKFBFLRUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PA2
Query on PA2

B PAROMOMYCIN (RING 2)
C6 H14 N2 O2
QOLDZWBHLDQIJR-FSIIMWSLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
P24
Query on P24

B 1-(AMINOETHYL)AMINO-4-AMINOBUTANE
PA(24) (Synonym)
C6 H17 N3
VRPPEXGZBZBARW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
42B
Query on 42B

B 4-AMINO-2-HYDROXYBUTANOIC ACID
C4 H9 N O3
IVUOMFWNDGNLBJ-GSVOUGTGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.298
  • R-Value Work: 0.251
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 32.80 α = 90.00
b = 46.55 β = 90.00
c = 88.81 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2002-12-17
  • Released Date: 2003-03-27
  • Deposition author(s): Russell, R., Murray, J.B.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4