3OWZ

Crystal structure of glycine riboswitch, soaked in Iridium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.210

Literature

Macromolecules
Sequence Display for 3OWZ

Classification: RNA

Total Structure Weight: 64700.41

Macromolecule Entities
Molecule Chains Length Organism Details
Domain II of glycine riboswitch A 88 synthetic
Domain II of glycine riboswitch B 88 synthetic

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

A, B IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLY
Query on GLY

A, B GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GLY N/A in BindingDB
N/A in BindingMoad
Kd: 3500 nM  PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
GDP
Query on GDP
A RNA LINKING C10 H15 N5 O11 P2 G
CCC
Query on CCC
A, B RNA LINKING C9 H13 N3 O10 P2 C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.210
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 82.61 α = 90.00
b = 82.61 β = 90.00
c = 149.55 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-09-20
  • Released Date: 2010-12-29
  • Deposition author(s): Huang, L., Serganov, A., Patel, D.J.

Revision History

  • Version 1_0: 2010-12-29

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2014-10-08

    Type: Structure summary