3SLM

Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine-5'-monophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 3SLM

Classification: RNA

Total Structure Weight: 46172.01

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (68-MER) A, B 68 synthetic

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

A, B 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SIN
Query on SIN

A SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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 %)
DGP N/A in BindingDB
N/A in BindingMoad
Kd: 379000 nM  PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
GTP
Query on GTP
A, B NON-POLYMER C10 H16 N5 O14 P3 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: 2.7 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.200
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 95.95 α = 90.00
b = 66.06 β = 117.95
c = 72.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-06-24
  • Released Date: 2011-08-17
  • Deposition author(s): Pikovskaya, O., Polonskaia, A., Patel, D.J., Serganov, A.A.

Revision History

  • Version 1_0: 2011-08-17

    Type: Initial release

  • Version 1_1: 2011-10-26

    Type: Database references