4G0U

Human topoisomerase IIbeta in complex with DNA and amsacrine

Structural Biology Knowledgebase: 4G0U SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.156

Literature

Macromolecules
Sequence Display for 4G0U

Classification: ISOMERASE / DNA / ISOMERASE INHIBITOR

Total Structure Weight: 196973.16


Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase 2-beta A, B 803 Homo sapiens EC#: 5.99.1.3 IUBMB
Fragment: HTOP2BETA CLEAVAGE CORE, UNP RESIDUES 450-1206
Gene Name(s): TOP2B Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') C, E 8 synthetic
DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3') D, F 12 synthetic

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

B, F N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide
Amsacrine (Synonym)
C21 H19 N3 O3 S
XCPGHVQEEXUHNC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, D, F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ASW EC50: 11000 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.156
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 80.92 α = 90.00
b = 175.80 β = 113.61
c = 93.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-10
  • Released Date: 2013-07-17
  • Deposition author(s): Wu, C.C., Li, T.K., Li, Y.C., Chan, N.L.

Revision History

  • 2014-03-12
    Type: Citation | Details: Citation update
  • 2013-10-02
    Type: Citation | Details: Citation update