3NP6

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

Structural Biology Knowledgebase: 3NP6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.301
  • R-Value Work: 0.236

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3NP6

Classification: DNA

Total Structure Weight: 7613.37

Macromolecule Entities
Molecule Chains Length Organism Details
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
BER
Query on BER

C BERBERINE
C20 H18 N O4
YBHILYKTIRIUTE-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: 2.3 Å
  • R-Value Free: 0.301
  • R-Value Work: 0.236
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 30.37 α = 90.00
b = 30.37 β = 90.00
c = 118.26 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2010-06-28
  • Released Date: 2011-05-04
  • Deposition author(s): Ferraroni, M., Bazzicalupi, C., Gratteri, P., Bilia, A.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4