4P1D | pdb_00004p1d

Structure of the complex of a bimolecular human telomeric DNA with Coptisine

• PDB DOI: https://doi.org/10.2210/pdb4P1D/pdb
• NAKB: 4P1D

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2014-02-26 Released: 2015-03-18 
• Deposition Author(s): Ferraroni, M., Bazzicalupi, C., Gratteri, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the complex of a bimolecular human telomeric DNA with Coptisine

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

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 7.95 kDa 
• Atom Count: 556 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
telomeric DNA	A, B	12	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KPT	E [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
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.567	α = 90
b = 41.567	β = 90
c = 66.157	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Ferraroni, M., Bazzicalupi, C., Gratteri, P.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description