1P59

Structure of a non-covalent Endonuclease III-DNA Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.214

Literature

Macromolecules
Sequence Display for 1P59

Classification: HYDROLASE / DNA

Total Structure Weight: 33545.55


Macromolecule Entities
Molecule Chains Length Organism Details
Endonuclease III A 226 Geobacillus stearothermophilus
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*AP*GP*AP*CP*GP*(5IU)P*GP*GP*AP*C)-3' B 11 synthetic
5'-D(TP*GP*(5IU)P*CP*CP*AP*(3DR)P*GP*(5IU)P*CP*T)-3' C 11 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SF4
Query on SF4

A IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
5IU
Query on 5IU
B, C DNA LINKING C9 H12 I N2 O8 P DU
3DR
Query on 3DR
C DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.214
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 66.32 α = 90.00
b = 105.90 β = 90.00
c = 41.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-25
  • Released Date: 2003-07-15
  • Deposition author(s): Fromme, J.C., Verdine, G.L.

Revision History

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