403D

5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE

Structural Biology Knowledgebase: 403D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.316
  • R-Value Work: 0.245

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 403D

Classification: DNA

Total Structure Weight: 7833.72

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*CP*(IGU)P*AP*AP*TP*TP*TP*GP*CP*G)-3') A, B 12 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HT1
Query on HT1

A 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)- 2,5'-BI-BENZIMIDAZOLE
HOECHST 33342 (Synonym)
C27 H28 N6 O
PRDFBSVERLRRMY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
IGU
Query on IGU
A, B DNA LINKING C10 H14 N5 O7 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.316
  • R-Value Work: 0.245
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 25.76 α = 90.00
b = 41.08 β = 90.00
c = 64.31 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1998-06-10
  • Released Date: 1998-07-06
  • Deposition author(s): Robinson, H., Gao, Y.-G., Bauer, C., Roberts, C., Switzer, C., Wang, A.H.-J.

Revision History

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