4GFH

Topoisomerase II-DNA-AMPPNP complex

Structural Biology Knowledgebase: 4GFH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.41 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.239

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GFH

Classification: Isomerase / DNA

Total Structure Weight: 305580.15


Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase 2 A, F 1177 Saccharomyces cerevisiae EC#: 5.99.1.3 IUBMB
Fragment: UNP RESIDUES 1-1177
Gene Name(s): TOP2 TOR3 YNL088W N2244
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3') B, G 11 synthetic
DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3') C, H 15 synthetic
DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3') D, I 11 synthetic
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3') E, J 15 synthetic

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

A, F PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
PTR
Query on PTR
A, F L-PEPTIDE LINKING C9 H12 N O6 P TYR
TSP
Query on TSP
D, I NON-POLYMER C10 H15 N2 O7 P S T

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.41 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.239
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 169.13 α = 90.00
b = 169.88 β = 90.00
c = 169.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-03
  • Released Date: 2012-10-03
  • Deposition author(s): Schmidt, B.H., Osheroff, N., Berger, J.M.

Revision History

  • 2012-12-12
    Type: Citation | Details: Citation update