4D9X | pdb_00004d9x

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

• PDB DOI: https://doi.org/10.2210/pdb4D9X/pdb
• NAKB: 4D9X

• Classification: DNA
• Mutation(s): No 


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

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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

Literature

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

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

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.6 kDa 
• Atom Count: 490 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')	A, B, C, D	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KPT	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	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 = 30.282	α = 90
b = 30.282	β = 90
c = 118.33	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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