1D3Y

STRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNIT

Structural Biology Knowledgebase: 1D3Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 1D3Y

Classification: ISOMERASE

Total Structure Weight: 68317.05

Macromolecule Entities
Molecule Chains Length Organism Details
DNA TOPOISOMERASE VI A SUBUNIT A, B 301 Methanocaldococcus jannaschii EC#: 5.99.1.3 IUBMB
Fragment: DNA BINDING CORE
Gene Name(s): top6A MJ0369
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.197
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 66.51 α = 90.00
b = 59.04 β = 94.05
c = 87.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-10-01
  • Released Date: 1999-11-05
  • Deposition author(s): Nichols, M.D., DeAngelis, K.A., Keck, J.L., Berger, J.M.

Revision History

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