5GWI

Structure of a Human topoisomerase IIbeta fragment in complex with DNA and E7873R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.214

Literature

Macromolecules
Sequence Display for 5GWI

Classification: ISOMERASE / DNA / ISOMERASE INHIBITOR

Total Structure Weight: 199294.59


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
N2N
Query on N2N

A, B N-[(5R,5aS,8aR,9R)-9-(3,5-dimethoxy-4-oxidanyl- phenyl)-8-oxidanylidene-5a,6,8a,9-tetrahydro- 5H-[2]benzofuro[5,6-f][1,3]benzodioxol-5- yl]-3-[(4R)-2,2-bis(chloranyl)-1,3-diaza- 2$l^{4}-platinacyclopent-4-yl]propanamide
C26 H29 Cl2 N3 O8 Pt
XOJFXYPXINBIDW-BFZFYWOISA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
N2R
Query on N2R

A, B ~{N}-[(5~{R},5~{a}~{S},8~{a}~{R},9~{R})-9- (3,5-dimethoxy-4-oxidanyl-phenyl)-8-oxidanylidene- 5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[5,6- f][1,3]benzodioxol-5-yl]-3-[(4~{S})-2,2-bis(chloranyl)- 1,3-diaza-2$l^{4}-platinacyclopent-4-yl]propanamide
C26 H29 Cl2 N3 O8 Pt
XOJFXYPXINBIDW-FTKFZVBUSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, D, 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: 2.74 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.214
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 79.79 α = 90.00
b = 176.97 β = 112.30
c = 94.53 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