1F1T

CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE

Structural Biology Knowledgebase: 1F1T SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.261

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1F1T

Classification: RNA

Total Structure Weight: 13756.41

Macromolecule Entities
Molecule Chains Length Organism Details
MALACHITE GREEN APTAMER RNA A 38 synthetic ALL URIDINES ARE 5-BROMO-URIDINE

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

A N,N'-TETRAMETHYL-ROSAMINE
(6-DIMETHYLAMINO-9-PHENYL-XANTHEN-3-YLIDENE)- DIMETHYL-AMMONIUM (Synonym)
C23 H23 N2 O
NGSXFKKYKWBNPO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SR
Query on SR

A STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ROS N/A in BindingDB
N/A in BindingMoad
Kd: 40 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
5BU
Query on 5BU
A RNA LINKING C9 H12 Br N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.261
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 55.30 α = 90.00
b = 55.30 β = 90.00
c = 143.92 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2000-05-19
  • Released Date: 2000-09-04
  • Deposition author(s): Baugh, C., Grate, D., Wilson, C.

Revision History

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