4FE5

Crystal structure of the xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine

Structural Biology Knowledgebase: 4FE5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4FE5

Classification: RNA

Total Structure Weight: 22727.82

Macromolecule Entities
Molecule Chains Length Organism Details
xpt-pbuX guanine riboswitch aptamer domain B 67 synthetic

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

B COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HPA
Query on HPA

B HYPOXANTHINE
C5 H4 N4 O
FDGQSTZJBFJUBT-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
HPA N/A in BindingDB
N/A in BindingMoad
Kd: 732 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.196
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 133.25 α = 90.00
b = 35.25 β = 90.75
c = 41.83 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2012-05-29
  • Released Date: 2012-06-27
  • Deposition author(s): Stoddard, C.D., Trausch, J.J., Widmann, J., Marcano, J., Knight, R., Batey, R.T.
  • Previous versions: 1U8D

Revision History

No revisions since initial release