3CDM

Structural adaptation and conservation in quadruplex-drug recognition

Structural Biology Knowledgebase: 3CDM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.234

Literature

Macromolecules
Sequence Display for 3CDM

Classification: DNA

Total Structure Weight: 18228.08

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*DT*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DG)-3') A, B 23 synthetic

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

A, B 2,7-bis[3-(dimethylamino)propyl]-4,9-bis[(3- hydroxypropyl)amino]benzo[lmn][3,8]phenanthroline- 1,3,6,8(2H,7H)-tetrone
C30 H42 N6 O6
XRDZCSQPAUGHQH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.234
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 39.58 α = 90.00
b = 43.08 β = 103.58
c = 56.94 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2008-02-27
  • Released Date: 2008-09-23
  • Deposition author(s): Parkinson, G.N., Neidle, S.

Revision History

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