1UHX

Crystal structure of d(GCGAGAGC): the base-intercalated duplex

Structural Biology Knowledgebase: 1UHX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1UHX

Classification: DNA

Total Structure Weight: 2799.42

Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*(CBR)P*GP*AP*GP*AP*GP*C)-3' A 8 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NCO
Query on NCO

A COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CBR
Query on CBR
A DNA LINKING C9 H13 Br N3 O7 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.220
  • Space Group: P 63 2 2

Unit Cell:

Length (Å) Angle (°)
a = 37.67 α = 90.00
b = 37.67 β = 90.00
c = 65.49 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2003-07-13
  • Released Date: 2004-02-03
  • Deposition author(s): Kondo, J., Umeda, S.I., Fujita, K., Sunami, T., Takenaka, A.

Revision History

  • 2014-10-22
    Type: Linkage | Details: remove incorrect links
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4