3L4K

Topoisomerase II-DNA cleavage complex, metal-bound

Structural Biology Knowledgebase: 3L4K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.239

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3L4K

Classification: Isomerase / DNA

Total Structure Weight: 104470.57


Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase 2 A 757 Saccharomyces cerevisiae EC#: 5.99.1.3 IUBMB
Fragment: RESIDUES 421-1177
Mutation: Y782X
Gene Name(s): TOP2 TOR3 YNL088W N2244
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3') B 11 synthetic
DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3') C 15 synthetic
DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*)-3') D 10 synthetic
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3') E 15 synthetic

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

D 3'-THIO-THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O7 P S
BORVFKJZAOEGOO-GJMOJQLCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, E ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PTR
Query on PTR
A L-PEPTIDE LINKING C9 H12 N O6 P TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.239
  • Space Group: P 21 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 86.06 α = 90.00
b = 91.85 β = 90.00
c = 115.94 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-12-20
  • Released Date: 2010-05-26
  • Deposition author(s): Schmidt, B.H., Burgin, A.B., Deweese, J.E., Osheroff, N., Berger, J.M.

Revision History

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