5GWJ

Structure of a Human topoisomerase IIbeta fragment in complex with DNA and E7873S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 5GWJ

Classification: ISOMERASE / DNA / ISOMERASE INHIBITOR

Total Structure Weight: 199160.84


Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase 2-beta A, B 803 Homo sapiens EC#: 5.99.1.3 IUBMB
Fragment: 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 construct
DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3') D, F 12 Synthetic construct

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
N2S
Query on N2S

A, B chloro{4,5-di(amino-kappaN)-N-[9-(4-hydroxy- 3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9- hexahydro-2H-furo[3',4':6,7]naphtho[2,3-d][1,3]dioxol- 5-yl]pentanamide}platinum
C26 H31 Cl N3 O8 Pt
UVMRTXMJNLJFNR-LCZKZCLKSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
N2W
Query on N2W

A, B chloro{4,5-di(amino-kappaN)-N-[9-(4-hydroxy- 3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9- hexahydro-2H-furo[3',4':6,7]naphtho[2,3-d][1,3]dioxol- 5-yl]pentanamide}platinum
C26 H31 Cl N3 O8 Pt
UVMRTXMJNLJFNR-JLXFAVSYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, E, F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.183
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 80.18 α = 90.00
b = 176.99 β = 111.50
c = 94.41 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-09-12
  • Released Date: 2017-08-23
  • Deposition author(s): Wang, Y.R., Chen, S.F., Wu, C.C., Chan, N.L.

Revision History

  • Version 1_0: 2017-08-23

    Type: Initial release

  • Version 1_1: 2017-11-08

    Type: Database references, Source and taxonomy

  • Version 2_0: 2017-12-13

    Type: Non-polymer description, Structure summary