4D9X

The crystal structure of Coptisine bound to DNA d(CGTACG)

Structural Biology Knowledgebase: 4D9X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.307
  • R-Value Work: 0.261

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4D9X

Classification: DNA

Total Structure Weight: 7597.32

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*TP*AP*CP*G)-3') A, B, C, D 6 synthetic

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

C 6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2- a]isoquinolin-5-ium
Coptisine (Synonym)
C19 H14 N O4
XYHOBCMEDLZUMP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.307
  • R-Value Work: 0.261
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 30.28 α = 90.00
b = 30.28 β = 90.00
c = 118.33 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2012-01-12
  • Released Date: 2013-01-23
  • Deposition author(s): Ferraroni, M., Bazzicalupi, C., Gratteri, P., Bilia, A.R.

Revision History

No revisions since initial release