4L5K | pdb_00004l5k

Crystal structure of the complex of DNA hexamer d(CGATCG) with Coptisine

• PDB DOI: https://doi.org/10.2210/pdb4L5K/pdb
• NAKB: 4L5K

• Classification: DNA
• Mutation(s): No 


• Deposited: 2013-06-11 Released: 2014-07-02 
• Deposition Author(s): Ferraroni, M., Bazzicalupi, C., Gratteri, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Work: 
  0.267 (Depositor), 0.267 (DCC) 
• R-Value Observed: 
  0.267 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of DNA hexamer d(CGATCG) with Coptisine

Ferraroni, M., Bazzicalupi, C., Gratteri, P.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 2.13 kDa 
• Atom Count: 147 
• Modeled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KPT	B [auth A]	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Work:  0.267 (Depositor), 0.267 (DCC) 
• R-Value Observed: 0.267 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.581	α = 90
b = 26.581	β = 90
c = 77.094	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Ferraroni, M., Bazzicalupi, C., Gratteri, P.

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description