4D9X | pdb_00004d9x

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 
    0.307 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.261 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.266 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KPTClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history. 


Literature

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

Ferraroni, M., Bazzicalupi, C., Gratteri, P., Bilia, A.R.

To be published.

Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
A, B, C, D
6N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KPT
Query on KPT
Download Ideal Coordinates CCD File 
F [auth C]6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2-a]isoquinolin-5-ium
C19 H14 N O4
XYHOBCMEDLZUMP-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
E [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free:  0.307 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.261 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.266 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.282α = 90
b = 30.282β = 90
c = 118.33γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KPTClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description