1PVG

Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II

Structural Biology Knowledgebase: 1PVG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1PVG

Classification: ISOMERASE

Total Structure Weight: 98197.80

Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase II A, B 418 Saccharomyces cerevisiae EC#: 5.99.1.3 IUBMB
Fragment: N-terminal ATPase region
Mutation: M49M, M81M, M119M, M177M, M208M, M219M, M312M, M349M, M392M, M400M
Gene Name(s): TOP2 TOR3 YNL088W N2244

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

A, B 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, B 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
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.206
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.46 α = 90.00
b = 71.08 β = 90.00
c = 216.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-27
  • Released Date: 2003-08-26
  • Deposition author(s): Classen, S., Olland, S., Berger, J.M.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4